Complete genome sequence of a simian immunodeficiency virus from a red-capped mangabey

ABSTRACT

The nucleotide sequence and deduced amino acid sequences of the complete genome of a simian immunodeficiency virus isolate from a red-capped mangabey are disclosed. The invention relates to the nucleic acids and peptides encoded by and/or derived from these sequences and their use in diagnostic methods and as immunogens.

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This is a divisional application of non-provisional application U.S. Ser. No. 09/206,551, filed Dec. 7, 1998.

FEDERAL FUNDING LEGEND

[0002] This work was funded by grants AI 38573-02; AI 27698-05; RO1 ai25291; and NO1 AI 35170 from the national institutes of health. Therefore, the government may have certain rights in the invention.

BACKGROUND OF THE INVENTION

[0003] 1. Field of the Invention

[0004] The present invention is in the field of virology. The invention relates to the nucleic acid sequence of the complete genome of the new simian immunodeficiency virus isolate from a red-capped mangabey, sivrcm, and nucleic acids derived therefrom. The invention also relates to peptides encoded by and/or derived from sivrcm nucleic acid sequences, and host cells containing these nucleic acid sequences and peptides. The invention also relates to diagnostic methods, kits and immunogens which employ the nucleic acids, peptides and/or host cells of the invention.

[0005] 2. Description of the Related Art

[0006] Phylogenetic analyses of simian immunodeficiency virus (SIV) isolates reveal that they belong to five distinct lineages of the lentivirus family of retroviruses (47). These five SIV lentiviral lineages form a distinct sub-group because primate viruses are more closely related to each other than to lentiviruses from non-primate hosts (47). Importantly, only simian species indigenous to the African continent are naturally infected (4, 13, 28, 35). Thus far, natural SIV infections in Africa have been documented in the sooty mangabey (SM) (Cercocebus torquatus atys) (sivsm strains), in Liberia (30), in Sierra Leone (4, 5), and the Ivory Coast (43); in all four sub-species of African green monkeys (agm) (Cercopithecus aethiops) (1, 21, 22, 25, 33, 34, 39) (sivagm strains), in eastern, central and western Africa; in the Sykes monkey (syk) (Cercopithecus mitis) (sivsyk strains) in Kenya (9); in the mandrill (mnd) (Mandrillus sphinx) (sivmmd strains) (38, 50) in Gabon; and in chimpanzees (cpz) (Pan troglodytes) (sivcpz strains) (19, 20, 41, 42) also from Gabon. Because these sivs and their simian hosts are highly divergent from each other and widely distributed across Africa, it is believed that the SIV family evolved and established itself in African simians long before acquired immunodeficiency syndrome (AIDS) appeared in humans (4, 15, 18, 19, 21, 30, 37, 47).

[0007] One common characteristic among all sivs is that none are associated with immunodeficiency or any other disease in their natural hosts (9, 13, 22, 28, 30, 35, 38). This finding is in marked contrast to AIDS, which occurs in humans and macaques infected with primate lentiviruses (2, 7, 8, 27, 35). This lack of disease in the natural SIV hosts may be an example of long-term evolution toward avirulence (16), which supports the hypothesis that SIV has infected African simians for a relatively long time.

[0008] Human AIDS is caused by two distinct primate lentiviruses, human immunodeficiency virus (HIV), types 1 and 2 (2, 7). Interestingly, the phylogeny of HIV is markedly different from SIV, because genetic analyses have shown that the human viruses do not represent separate sixth and seventh lineages of primate lentiviruses, but instead, are members of two of the five existing SIV lineages (37, 46). HIV-1 is in the HIV-1/sivcpz group (19, 51) and HIV-2 belongs to the HIV-2/sivsm family (18, 23). These phylogenetic data on the HIV-1 and HIV-2 lineages have long suggested separate simian origins for HIV-1 and HIV-2 (37, 46).

[0009] Molecular studies of naturally occurring sivsm and HIV-2 strains from rural West Africa have provided convincing evidence for a simian origin of HIV-2. A close genetic relationship has been established between the HIV-2 D and E sub-types and sivsm strains found in household pet sooty mangabeys in West Africa (4, 14, 15). Moreover, all six known subtypes of HIV-2, including a new subtype F (3), are found only within the natural range of SIV-infected sooty mangabeys in West Africa. No other area of Africa or of the world has all six known HIV-2 subtypes. Together, these data provide strong support for independent transmissions of sivsm from naturally infected sooty mangabeys to humans.

[0010] In contrast, there is much less information to support a simian origin for HIV-1. Although sivcpz is the closest relative to HIV-1, there are only a few isolates, thus raising questions as to the likely primate reservoir. Only three sivcpz strains have thus far been identified (20, 41, 42, 51). The first one was isolated from a single, household pet chimpanzee in Gabon and was not part of a primate research colony (42). An additional sivcpz strain was found in a captive chimpanzee which was wild caught in Zaire and thus likely infected in Africa (41, 51). Finally, PCR data suggested the existence of a third sivcpz strain, again from a wild caught chimpanzee from Gabon (20). Thus, although based on limited data, the hypothesis that HIV-1 is derived from members of a larger sivcpz lineage remains plausible. However, additional sivs within the HIV-1/sivcpz lineage must be found to better understand the origin of the HIV-1 family.

[0011] The present invention is based on the genetic characterization of a new SIV isolate from a red-capped mangabey (RCM), Cercocebus torquatus torquatus. This RCM was a household pet in Lambarene, Gabon, and was not part of a primate colony, a zoo, or a research facility. Analysis of the full-length sequence of the sivrcm indicates that this virus is related to SIV from sooty mangabeys, albeit very distantly. Its genome organization contains a vpx gene which is unique to members of the sivsm/HIV-2 lineage. There is also phylogenetic evidence that sivrcm is a recombinant.

[0012] The sivrcm sequence(s) described herein will permit the development of new serological screening assays for testing of sivrcm infection of humans. Although such infections have not yet been documented, it should be noted that viruses from a second mangabey species (sivs from sooty mangabeys) have crossed the species barrier and have yielded a new human AIDS virus (HIV-2). It is thus conceivable that sivrcm is similarly infecting humans in Gabon and Cameroon. To test this possibility, strain specific reagents (antigens, polypeptides, etc.) Are required to test for sivrcm specific antibodies in people as a sign of viral infection. Such strain specific antigens can now be designed on the basis of the sivrcm sequence(s) described herein.

[0013] If evidence is found that humans in Africa are infected with sivrcm (regardless whether this infection is pathogenic or not), then new screening assays for the world's blood supply will have to be developed that specifically detect anti-sivrcm antibodies or sivrcm nucleic acids. Sivrcm sequences are necessary to design such strain-specific tests. Additionally, the new sequences will permit the development of assays for screening of primates, such as those in the wild, in zoos, and in research facilities, for sivrcm.

SUMMARY OF THE INVENTION

[0014] The present invention pertains to the isolation and characterization of the genomic sequence of sivrcm, a new simian immunodeficiency virus identified from a Gabonese red-capped mangabey (RCM), and nucleic acids derived therefrom. In particular, the present invention relates to nucleic acids comprising the complete genomic sequence of sivrcm, as well as nucleic acids comprising the complementary (or antisense) sequence of the genomic sequence of sivrcm, and nucleic acids derived therefrom.

[0015] The invention also relates to vectors comprising the nucleic acid genomic sequence of sivrcm, as well as nucleic acids comprising the complementary (or antisense) sequence of the genomic sequence of sivrcm, and nucleic acids derived therefrom.

[0016] The invention also relates to cultured host cells comprising the nucleic acid genomic sequence of sivrcm, as well as nucleic acids comprising the complementary (or antisense) sequence of the genomic sequence of sivrcm, and nucleic acids derived therefrom.

[0017] The invention also relates to host cells containing vectors comprising the genomic sequence of sivrcm, as well as nucleic acids comprising the complementary (or antisense) sequence of the genomic sequence of sivrcm, and nucleic acids derived therefrom.

[0018] The invention also relates to synthetic or recombinant polypeptides encoded by or derived from the nucleic acid sequence of the genome of sivrcm, and fragments thereof.

[0019] The invention also relates to methods for producing the polypeptides of the invention in culture using the sivrcm virus or nucleic acids derived therefrom, including recombinant methods for producing the polypeptides of the invention.

[0020] The invention further relates to methods of using the polypeptides of the invention as immunogens to stimulate an immune response in a mammal, such as the production of antibodies, or the generation of cytotoxic or helper T-lymphocytes.

[0021] The invention also relates to methods of using the polypeptides of the invention to detect antibodies which immunologically react with the sivrcm virion and/or its encoded polypeptides, in a mammal or in a biological sample.

[0022] The invention also relates to kits for the detection of antibodies specific for sivrcm in a biological sample where said kit contains at least one polypeptide encoded by or derived from the sivrcm nucleic acid sequences of the invention.

[0023] The invention also relates to antibodies which immunologically react with the sivrcm virion and/or its encoded polypeptides.

[0024] The invention also relates to methods of detecting sivrcm virion and/or its encoded polypeptides, or fragments thereof, using the antibodies of the invention.

[0025] The invention also relates to kits for detecting sivrcm virion, and/or its encoded polypeptides, wherein the kit comprises at least one antibody of the invention.

[0026] The invention also relates to a method for detecting the presence of sivrcm virus in a mammal or a biological sample, said method comprising analyzing the DNA or RNA of a mammal or a sample for the presence of the rnas, cdnas or genomic dnas which will hybridize to a nucleic acid derived from sivrcm. Usually, when a completely complementary probe is used, high stringency conditions are desirable in order to prevent false positives. However, conditions of high stringency should only be used if the probes are complementary to target regions which lack heterogeneity. The stringency of hybridization is determined by a number of factors during hybridization and during the washing procedure, including temperature, ionic strength, length of time, and concentration of formamide, if any. The nucleic acid sequences used in probes should be unique to sivrcm, i.e., The nucleic acid sequences should be absent from individual mammals not infected with sivrcm.

[0027] The invention also provides diagnostic kits for the detection of sivrcm in a mammal using the nucleic acids of the invention. In one embodiment, the kit comprises nucleic acids having sequences useful as hybridization probes in determining the presence or absence of sivrcm RNA, cdna or genomic DNA. In another embodiment, the kit comprises nucleic acids having sequences useful as primers for reverse-transcription polymerase chain reaction (RT-PCR) analysis of RNA for the presence of sivrcm in a biological sample.

[0028] The invention further relates to isolated and substantially purified nucleic acids, polypeptides and/or antibodies of the invention.

[0029] The invention further relates to compositions comprising one or more of the nucleic acids, polypeptides and/or antibodies of the invention.

BRIEF DESCRIPTION OF THE FIGURES

[0030]FIG. 1. PCR primer pairs and sequencing strategy.

[0031]FIG. 2. Alignment of amino acid sequences of env proteins of sivrcm and other primate lentiviruses. The homologies among the sequences are indicated by dashes. Sequences of amino acids which are uniquely present in the various polypeptides (as compared to the corresponding amino acids of the sivrcm) are indicated by letters, i.e., The sequences themselves.

[0032]FIG. 3. Genomic organization of sivrcm. Schematic diagram of the three possible reading frames of the sivrcm genome. The location of stop codons are indicated by vertical lines, and the locations of the sivrcm genes are indicated.

[0033]FIG. 4. Duplication of the TAR stemloop structure in the sivrcm LTR.

[0034]FIG. 5. Phylogenetic analysis of sivrcm. (A) gag; (B) pol (5′ end); (C) env; and (D) nef genes. Phylogenies indicate discordant branching orders which strongly suggest a recombinant sivrcm genome.

[0035]FIG. 6. Alignment of the putative polypeptide products of the extended rev orfs in sivsm and sivrcm. Asterisks denote stop codons. Conservative amino acid changes are indicated as a colon (:); a vertical line depicts the position of the splice donor.

[0036]FIG. 7. Amino acid sequence alignment of the “extended rev ORF” in members of the HIV-2/sivsm/sivmac group. The vertical line indicates the position of the splice donor, usually used to express the spliced versions of tat and rev, respectively. Stop codons are indicated as asterisks. All sivsm/sivmac strains as well as HIV-2/FO784 have an uninterrupted extended rev ORF.

[0037]FIG. 8. Nucelotide sequence of the sivrcm genome (SEQ ID NO:1)

[0038]FIG. 9. Deduced amino acid sequence of the sivrcm Gag protein.

[0039]FIG. 10. Deduced amino acid sequence of the sivrcm Pol protein.

[0040]FIG. 11. Deduced amino acid sequence of the sivrcm Vif protein.

[0041]FIG. 12. Deduced amino acid sequence of the sivrcm Vpx protein.

[0042]FIG. 13. Deduced amino acid sequence of the sivrcm Vpr protein.

[0043]FIG. 14. Deduced amino acid sequence of the sivrcm Tat protein.

[0044]FIG. 15. Deduced amino acid sequence of the sivrcm Rev protein.

[0045]FIG. 16. Deduced amino acid sequence of the sivrcm Env protein.

[0046]FIG. 17. Deduced amino acid sequence of the sivrcm Nef protein.

[0047]FIG. 18. Partial nucleotide sequence of sivrcm gag gene and deduced amino acid sequence.

[0048]FIG. 19. Partial nucleotide sequence of sivrcm pol gene and deduced amino acid sequence.

DETAILED DESCRIPTION OF THE INVENTION

[0049] The present invention relates to the determination of the nucleic acid sequence of the complete genome of sivrcm, an isolate of simian immunodeficiency virus identified from a Gabonese red-capped mangabey (RCM) and nucleic acids derived therefrom. The nucleotide sequence of the sivrcm is shown in the sequence listing as SEQ ID NO: 1.

[0050] The phrase “derived from” is used throughout the specification and claims with respect to nucleic acids to describe nucleic acid sequences which correspond to a region of the designated nucleotide sequence. Preferably, the sequence of the region from which the nucleic acid is derived is, or is complementary to, a sequence which is unique to the sivrcm genome. Whether or not a sequence is unique to the genome of sivrcm can be determined by techniques known to those of skill in the art. For example, the sequence can be compared to sequences in databanks, e.g., Genbank, to determine whether it is present in the uninfected host or other organisms. The sequence can also be compared to the known sequences of other viral agents, including other retroviruses. The correspondence or non-correspondence of the derived sequence to other sequences can also be determined by hybridization under the appropriate stringency conditions. Hybridization techniques for determining the complementarity of nucleic acid sequences are well known in the art. In addition, mismatches of duplex polynucleotides formed by hybridization can be determined by known techniques, including for example, digestion with a nuclease such as S1 that specifically digests single-stranded areas in duplex polynucleotides.

[0051] Regions of the viral genome from which nucleic acid sequences may be derived include, but are not limited to, regions encoding specific epitopes as well as non-transcribed and non-translated sequences. Preferably, the epitope is unique to a polypeptide encoded by the sivrcm genome. The uniqueness of the epitope may be determined by its degree of immunological cross-reactivity with other SIV viruses. Methods for determining immunological cross-reactivity are known in the art, e.g., Radioimmunoassay and ELISA and other assays mentioned herein. The uniqueness of an epitope can also be determined by computer searches of known databases, e.g., For the polynucleotide sequences which encode the epitope, and by amino acid sequence comparisons with other known proteins.

[0052] The derived nucleic acid is not necessarily physically derived from the nucleotide sequence shown, but may be generated in any manner, including for example, chemical synthesis or DNA replication or reverse transcription or transcription, which are based on the information provided by the sequence of bases in the region(s) from which the nucleic acid is derived. The derived nucleic acid is comprised of at least 6-12 bases, more preferably at least 15-19 bases, more preferably at least 30 bases. The derived nucleic acid may also be larger, e.g., At least 100 bases in length, depending on the desired use of the nucleic acid. In addition, regions or combinations of regions corresponding to that of the designated sequence may be modified in ways known in the art to be consistent with an intended use. The derived nucleic acid may be a polynucleotide or polynucleotide analog.

[0053] The term “recombinant nucleotide” or “recombinant nucleic acid” as used herein intends a nucleic acid of genomic, cdna, semisynthetic, or synthetic origin which, by virtue of its origin or manipulation: (1) is not associated with all or a portion of the nucleic acid with which it is associated in nature; and/or (2) is linked to a nucleic acid other than that to which it is linked in nature.

[0054] The term “polynucleotide” as used herein refers to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. This term refers only to the primary structure of the molecule. Thus, this term includes double- and single-stranded DNA, as well as double- and single-stranded RNA. It also includes modified, for example, by methylation and/or by capping, and unmodified forms of the polynucleotide.

[0055] The present invention relates to nucleic acids having the entire genomic sequence of the sivrcm isolate as shown in SEQ ID NO:1, as well as fragments (or partial sequences) thereof. The invention also relates to nucleic acids having complementary (or antisense) sequences of the sequence shown in SEQ ID NO:1, as well as fragments (or partial sequences) thereof. Partial sequences may be obtained by various methods, including restriction digestion of the complete sequence of sivrcm, PCR amplification, and direct synthesis. Partial sequences may be all or part of the LTR and/or other untranslated regions of the sivrcm genome, and/or all or part of the genes encoding the Gag, Pol, Vif, Vpr, Env, Tat, Rev, Nef and Vpx proteins and/or complementary (or antisense) sequences thereof. Nucleic acids of the invention also include cdna, mrna, and other nucleic acids derived from the sivrcm genomic sequence. Sequences of the ltrs and of the genes encoding Gag, Pol, Vif, Vpr, Env, Tat, Rev, Nef and Vpx are identified in FIGS. 9 to 17. Partial sequences of sivrcm gag and pol genes and encoded amino acid sequence are shown in FIGS. 18 and 19. These latter sequences are available in genbank, having Accession Numbers AF028608 and AF028607, respectively. Minor sequence variations between SEQ ID NO:1 and the pol gene of FIG. 19 are due to the fact that this partial pol gene sequence (in addition to the partial gag gene sequence) was obtained from a different clone of sivrcm than that represented by SEQ ID NO: 1.

[0056] The nucleic acids of the invention may be present in vectors or host cells in tissue culture or other media. The nucleic acids of the invention may also be isolated and substantially purified, by methods known in the art.

[0057] Nucleic acids of about 17 bases to about 35 bases in length are particularly preferred for use as primers in PCR amplification (see, e.g., The primers gag A and gag B (25mer and 32mer respectively)). Nucleic acids of about 14 to about 25 bases in length are particularly preferred for use in nucleotide arrays. (See, e.g., Ref. 80, which uses 20 to 25 mers).

[0058] The present invention also relates to vectors and host cells comprising the nucleic acids of the invention.

[0059] The present invention also relates to compositions comprising one or more of the nucleic acids, vectors, and/or host cells of the invention.

[0060] The present invention further relates to methods of using the nucleic acids, vectors, and/or host cells of the invention, and/or compositions thereof. For example, the invention relates to the use of nucleic acids of the invention as diagnostic agents to detect the presence or absence of sivrcm in a sample.

[0061] The present invention also relates to a method for detecting the presence of sivrcm in a mammal using the nucleic acids of this invention.

[0062] In one embodiment, the detection method involves analyzing DNA of a mammal suspected of harboring sivrcm. DNA can be isolated by methods well known in the art.

[0063] The methods for analyzing the DNA for the presence of sivrcm include Southern blotting (63), dot and slot hybridization (60), and nucleotide arrays (see, e.g., U.S. Pat. No. 5,445,934 and U.S. Pat. No. 5,733,729).

[0064] The nucleic acid probes used in the detection methods set forth above are derived from the nucleic acid sequence shown in SEQ ID NO: 1. The size of such probes is at least 10-12 bases long, more usually at least about 19 bases long, more usually from about 200 to about 500 bases, and often exceeding about 1000 bases.

[0065] The nucleic acid probes of this invention may be DNA or RNA. Nucleic acids can be synthesized using any of the known methods of nucleotide synthesis (see, e.g., Refs. 54, 55, 58), or they can be isolated fragments of naturally occurring or cloned DNA. In addition, those skilled in the art would be aware that nucleotides can be synthesized by automated instruments sold by a variety of manufacturers or can be commercially custom ordered and prepared. The probes of this invention may also be nucleotide analogs, such as nucleotides linked by phosphodiester, phosphorothiodiester, methylphosphonodiester, or methylphosphonothiodiester moieties (67) and peptide nucleic acids (pnas), in which the sugar-phosphate backbone of the polynucleotide is replaced with a polyamide or “pseudopeptide” backbone (68).

[0066] The nucleic acid probes can be labeled using methods known to one skilled in the art. Such labeling techniques can include radioactive labels, biotin, avidin, enzymes and fluorescent molecules (62).

[0067] The nucleic acid probes used in the detection methods set forth above are derived from sequences substantially homologous to the sequence shown in SEQ ID NO:1, or its complementary sequence. By “substantially homologous”, as used throughout the specification and claims to describe the nucleic acid sequences of the present invention, is meant a high level of homology between the nucleic acid sequence and the sequence of SEQ ID NO:1, or its complementary sequence. Preferably, the level of homology is in excess of 80%, more preferably in excess of 90%, with a preferred nucleic acid sequence being in excess of 95% homologous with a portion of SEQ ID NO:1, or its complement. The size of such probes is usually at least 20 nucleotides, more usually from about 200 to 500 nucleotides, and often exceeding 1000 nucleotides.

[0068] Although complete complementarity is not necessary, it is preferred that the probes are made completely complementary to the corresponding portion of the sivrcm genome, mrna or cdna target.

[0069] The probes can be packaged into diagnostic kits. Diagnostic kits may include ingredients for labelling and other reagents and materials needed for the particular hybridization protocol in addition to the probes.

[0070] In another embodiment of the invention, the detection method comprises analyzing the RNA of a mammal for the presence of sivrcm. RNA can be isolated by methods well known in the art.

[0071] The methods for analyzing the RNA for the presence of sivrcm include Northern blotting (66), dot and slot hybridization, filter hybridization (57), rnase protection (62), and reverse-transcription polymerase chain reaction (RT-PCR) (65). A preferred method is RT-PCR. In this method, the RNA can be reverse transcribed to first strand cdna using a nucleic acid primer or primers derived from the nucleotide sequence shown in SEQ ID NO:1. Once the cdnas are synthesized, PCR amplification is carried out using pairs of primers designed to hybridize with sequences in the genome of sivrcm which are an appropriate distance apart (at least about 50 bases) to permit amplification of the cdna and subsequent detection of the amplification product. Each primer of a pair is a single-stranded nucleic acid of about 20 to about 60 bases in length where one primer (the “upstream” primer) is complementary to the original RNA and the second primer (the “downstream” primer) is complementary to the first strand of cdna generated by reverse transcriptions of the RNA. The target sequence is generally about 100 to about 300 bases in length but can be as large as 500-1500 bases or more, e.g., 9,000 bases. Optimization of the amplification reaction to obtain sufficiently specific hybridization to the sivrcm nucleotide sequence is well within the skill in the art and is preferably achieved by adjusting the annealing temperature.

[0072] The amplification products of PCR can be detected either directly or indirectly. In one embodiment, direct detection of the amplification products is carried out via labeling of primer pairs. Labels suitable for labeling the primers of the present invention are known to one skilled in the art and include radioactive labels, biotin, avidin, enzymes and fluorescent molecules. The desired labels can be incorporated into the primers prior to performing the amplification reaction. Alternatively, the desired labels can be incorporated into the primer extension products during the amplification reaction in the form of one or more labeled dntps. In one embodiment of the present invention, the labeled amplified PCR products can be detected by agarose gel electrophoresis followed by ethidium bromide staining and visualization under ultraviolet light or via direct sequencing of the PCR-products. The labeled amplified PCR products can also be detected by binding to immobilized oligonucleotide arrays.

[0073] In yet another embodiment, unlabelled amplification products can be detected via hybridization with labeled nucleic acid probes in methods known to one skilled in the art, such as dot or slot blot hybridization or filter hybridization.

[0074] The invention also relates to methods of using these nucleic acids to produce polypeptides in vitro or in vivo. In one embodiment of the invention, a recombinant method of making a polypeptide of the invention comprises:

[0075] a) preparing of a nucleic acid capable of directing a host cell to produce a polypeptide encoded by the sivrcm genome;

[0076] b) cloning the nucleic acid into a vector capable of being transferred into and replicated in a host cell, such vector containing operational elements for expressing the nucleic acid, if necessary;

[0077] c) transferring the vector containing the nucleic acid and operational elements into a host cell capable of expressing the polypeptide;

[0078] d) growing the host under conditions appropriate for expression of the polypeptide; and

[0079] d) harvesting the polypeptide.

[0080] The present invention also relates to non-recombinant methods of making the polypeptides and nucleic acids of the invention. In addition to synthetic methods, the non-recombinant methods involve culturing sivrcm in cell lines, preferably in uninfected human peripheral blood mononuclear cells, under conditions appropriate for expression of the polypeptides and nucleic acids. This invention thus also relates to the polypeptides and nucleic acids produced by the virus in cell culture. The polypeptides and nucleic acids may be isolated and purified by methods known in the art.

[0081] The vectors contemplated for use in the present invention include any vectors into which a nucleic acid sequence as described above can be inserted, along with any preferred or required operational elements, and which vector can then be subsequently transferred into a host cell and, preferably, replicated in such cell. Preferred vectors are those whose restriction sites have been well documented and which contain the operational elements preferred or required for transcription of the nucleic acid sequence. Vectors may also be used to prepare large amounts of nucleic acids of the invention, which may be used, e.g., To prepare probes or other nucleic acid constructs.

[0082] When expression of a polypeptide is desired, the “operational elements” as discussed herein include at least one promoter sequence capable of initiating transcription of the nucleic acid sequence, at least one leader sequence, at least one terminator codon and/or termination signal, and any other DNA sequences necessary or preferred for appropriate transcription and subsequent translation of the vector nucleic acid. In particular, it is contemplated that such vectors will preferably contain at least one origin of replication recognized by the host cell along with at least one selectable marker.

[0083] Preferred expression vectors of this invention are those which function in bacterial and/or eukaryotic cells. Examples of vectors which function in eukaryotic cells include, but are not limited to Venezuelan equine encephalitis virus vectors, simian virus vectors, vaccinia virus vectors, adenovirus vectors, herpes virus vectors, or vectors based on retroviruses, such as murine leukemia virus, or HIV or other lentivirus (76).

[0084] The selected expression vector may be transfected into a suitable bacterial or eukaryotic cell system for purposes of expressing the recombinant polypeptide. Eukaryotic cell systems include but are not limited to cell lines such as hela, COS-1, 293T, MRC-5, or CV-1 cells. Primary human cells, such as lymph node cells, macrophages, etc., Are also useful in practicing the invention.

[0085] The expressed polypeptides may be detected directly by methods known in the art including, but not limited to, Coomassie blue staining and Western blotting or indirectly, such as in detection of the expression product of a reporter gene, such as luciferase.

[0086] In another embodiment of the invention, the method comprises administering a composition comprising a vector comprising a nucleic acid of the invention to a mammal to produce a polypeptide in vivo.

[0087] The present invention also relates to polypeptides encoded by and/or derived from the nucleotide sequences of this invention. These polypeptides may be natural, synthetic or produced by recombinant methods. Polypeptides can be obtained as a crude lysate or can be purified by standard protein purification procedures known in the art which may include differential precipitation, molecular sieve chromatography, ion-exchange chromatography, isoelectric focusing, gel electrophoresis and affinity and immunoaffinity chromatography. The polypeptides may be purified by passage through a column containing a resin which has bound thereto antibodies specific for an open reading frame (ORF) polypeptide. The present invention also relates to compositions comprising one or more of the polypeptides of the invention.

[0088] A polypeptide or amino acid sequence derived from a designated nucleic acid sequence refers to a polypeptide having an amino acid sequence identical to that of a polypeptide encoded by the sequence, or a portion thereof wherein the portion consists of at least 6-8 amino acids, and more preferably at least 10 amino acids, and more preferably at least 11-15 amino acids, and most preferably at least 30 amino acids or which is immunologically cross-reactive with a polypeptide encoded by the sequence. The polypeptide may also be larger, e.g., At least 100 amino acids in length, depending on the desired use of the polypeptide. Polypeptides from the V3-loop region and the “crown” of gp41 of Env are particularly preferred.

[0089] A recombinant or derived polypeptide is not necessarily translated from a designated nucleic acid sequence; it may be generated in any manner, including for example, chemical synthesis, or expression of a recombinant expression system, or isolation from sivrcm.

[0090] It should be noted that the nucleotide sequences described herein represent one embodiment of the present invention. Due to the degeneracy of the genetic code, it is to be understood that numerous choices of nucleotides may be made that will lead to a sequence capable of directing production of the polypeptides set forth above. As such, nucleic acid sequences which are functionally equivalent to the sequences described herein are intended to be encompassed within the present invention. For example, preferred codons which are appropriate to the host cell may be used (see, e.g., WO 98/34640), or the sequence may be modified to reduce the effect of any inhibitory/instability sequences and to provide for Rev-independent gene expression (77).

[0091] The polypeptides of this invention consist of at least 6-12 amino acids, more preferably at least 13-18 amino acids, even more preferably at least 19-24 amino acids and most preferably at least 25-30 amino acids encoded by, or otherwise derived from, the sivrcm genomic sequence.

[0092] The present invention further relates to the use of polypeptides of the invention as diagnostic agents. In one embodiment, the polypeptides of the invention can be used in immunoassays for detecting the presence of antibodies against sivrcm in a mammal and for diagnosing the presence of sivrcm infection in a mammal. For the purposes of the present invention, “mammal” as used throughout the specification and claims, includes, but is not limited to humans, chimpanzees, mangabeys, other primates and the like.

[0093] In a preferred embodiment, test serum is reacted with a solid phase reagent having a surface-bound polypeptide of this invention as an antigen. The solid surface reagent can be prepared by known techniques for attaching polypeptides to solid support material. These attachment methods include non-specific adsorption of the polypeptide to the support or covalent attachment of the polypeptide to a reactive group on the support. After reaction of the antigen with an antibody against any one of the viruses of this invention in the serum, unbound serum components are removed by washing and the antigen-antibody complex is reacted with a secondary antibody such as labeled anti-human antibody. The label may be an enzyme which is detected by incubating the solid support in the presence of a suitable fluorimetric or calorimetric reagent. Other detectable labels may also be used, such as radiolabels or colloidal gold, and the like.

[0094] Immunoassays of the present invention may be a radioimmunoassay, Western blot assay, immunofluorescent assay, enzyme immunoassay, chemiluminescent assay, immunohistochemical assay and the like. Standard techniques for ELISA are well known in the art. Such assays may be a direct, indirect, competitive, or noncompetitive immunoassay as described in the art (see, e.g., Ref. 61). Biological samples appropriate for such detection assays include, but are not limited to serum, liver, saliva, lymphocytes or other mononuclear cells.

[0095] Polypeptides of the invention may be prepared in the form of a kit, alone, or in combinations with other reagents such as secondary antibodies, for use in immunoassays. In yet another embodiment, the polypeptides of the invention can be used as immunogens to raise antibodies and/or stimulate cellular immunity in a mammal.

[0096] The immunogen may be a partially or substantially purified peptide. Alternatively, the immunogen may be a cell, cell lysate from cells transfected with a recombinant expression vector, or a culture supernatant containing the expressed polypeptide. The immunogen may comprise one or more structural proteins, and/or one or more non-structural proteins of sivrcm, or a mixture thereof.

[0097] The effective amount of polypeptide per unit dose sufficient to induce an immune response depends, among other things, on the species of mammal inoculated, the body weight of the mammal and the chosen inoculation regimen, as well as the presence or absence of an adjuvant, as is well known in the art. Inocula typically contain polypeptide concentrations of about 1 microgram to about 50 milligrams per inoculation (dose), preferably about 10 micrograms to about 10 milligrams per dose, most preferably about 100 micrograms to about 5 milligrams per dose.

[0098] The term “unit dose” as it pertains to the inocula refers to physically discrete units suitable as unitary dosages for mammals, each unit containing a predetermined quantity of active material (polypeptide) calculated to produce the desired immunogenic effect in association with the required diluent. Inocula are typically prepared as a solution in a physiologically acceptable carrier such as saline, phosphate-buffered saline and the like to form an aqueous pharmaceutical composition. The route of inoculation of the polypeptides of the invention is typically parenteral and is preferably intramuscular, subcutaneous and the like. The dose is administered at least once. In order to increase the antibody level, at least one booster dose may be administered after the initial injection, preferably at about 4 to 6 weeks after the first dose. Subsequent doses may be administered as indicated.

[0099] To monitor the antibody response of individuals administered the compositions of the invention, antibody titers may be determined. In most instances it will be sufficient to assess the antibody titer in serum or plasma obtained from such an individual. Decisions as to whether to administer booster inoculations or to change the amount of the composition administered to the individual may be at least partially based on the titer. The titer may be based on an immunobinding assay which measures the concentration of antibodies in the serum which bind to a specific antigen. The ability to neutralize in vitro and in vivo biological effects of sivrcm may also be assessed to determine the effectiveness of the immunization.

[0100] For all therapeutic, prophylactic and diagnostic uses, the polypeptide of the invention, alone or linked to a carrier, as well as antibodies and other necessary reagents and appropriate devices and accessories may be provided in kit form so as to be readily available and easily used. Where immunoassays are involved, such kits may contain a solid support, such as a membrane (e.g., Nitrocellulose), a bead, sphere, test tube, microtiter well, rod, and so forth, to which a receptor such as an antibody specific for the target molecule will bind. Such kits can also include a second receptor, such as a labelled antibody. Such kits can be used for sandwich assays. Kits for competitive assays are also envisioned.

[0101] The immunogens of this invention can also be generated by the direct administration of nucleic acids of this invention to a subject. DNA-based vaccination has been shown to stimulate humoral and cellular responses to HIV-1 antigens in mice (69-72) and macaques (72, 73). More recent studies in infected chimpanzees have shown a possible application of this strategy in HIV-1-infected humans: DNA vaccination of HIV-1-infected chimpanzees with a construct that drives expression of HIV-1 env and rev appeared well-tolerated, and immunized animals demonstrated a boost in antibody response followed by a >1 log decrease in their virus loads (74). A DNA-based vaccine containing HIV-1 env and rev genes was injected into HIV-infected human patients in three doses (30, 100 or 300 micrograms) at 10-week intervals. Increased antibodies against gp120 were observed in the 100 and 300 μg groups. Increases were also noted in cytotoxic T lymphocyte (CTL) activity against gp160-bearing targets and in lymphocyte proliferative activity (78, 79).). DNA-based vaccines containing HIV gag genes, with modification of the viral nucleotide sequence to incorporate host-preferred codons (see, e.g., WO 98/34640), and/or to reduce the effect of inhibitory/instability sequences (see, e.g., Ref. 77), have likewise been described.

[0102] Therefore, it is anticipated that the direct injection of RNA or DNA vectors of this invention encoding viral antigen can be used for endogenous expression of the antigen to generate the viral antigen for presentation to the immune system without the need for self-replicating agents or adjuvants, resulting in the generation of antigen-specific ctls and protection from a subsequent challenge with a homologous or heterologous strain of virus.

[0103] Ctls in both mice and humans are capable of recognizing epitopes derived from conserved internal viral proteins and are thought to be important in the immune response against viruses. By recognition of epitopes from conserved viral proteins, ctls may provide cross-strain protection. Ctls specific for conserved viral antigens can respond to different strains of virus, in contrast to antibodies, which are generally strain-specific.

[0104] Thus, direct injection of RNA or DNA encoding the viral antigen has the advantage of being without some of the limitations of direct peptide delivery or viral vectors (see, e.g., Ref. 81 and the discussions and references therein). Furthermore, the generation of high-titer antibodies to expressed proteins after injection of DNA indicates that this may be a facile and effective means of making antibody-based vaccines targeted towards conserved or non-conserved antigens, either separately or in combination with CTL vaccines targeted towards conserved antigens. These may also be used with traditional peptide vaccines, for the generation of combination vaccines. Furthermore, because protein expression is maintained after DNA injection, the persistence of B and T cell memory may be enhanced, thereby engendering long-lived humoral and cell-mediated immunity.

[0105] Nucleic acids encoding a sivrcm polypeptide of this invention can be introduced into animals or humans in a physiologically or pharmaceutically acceptable carrier using one of several techniques such as injection of DNA directly into human tissues; electroporation or transfection of the DNA into primary human cells in culture (ex vivo), selection of cells for desired properties and reintroduction of such cells into the body, (said selection can be for the successful homologous recombination of the incoming DNA to an appropriate preselected genomic region); generation of infectious particles containing the sivrcm gag and/or other sivrcm genes, infection of cells ex vivo and reintroduction of such cells into the body; or direct infection by said particles in vivo. Substantial levels of polypeptide will be produced leading to an efficient stimulation of the immune system.

[0106] Also envisioned are therapies based upon vectors, such as viral vectors containing nucleic acid sequences coding for the polypeptides described herein. These molecules, developed so that they do not provoke a pathological effect, will stimulate the immune system to respond to the polypeptides.

[0107] The effective amount of nucleic acid immunogen per unit dose to induce an immune response depends, among other things, on the species of mammal inoculated, the body weight of the mammal and the chosen inoculation regimen, as is well known in the art. Inocula typically contain nucleic acid concentrations of about 1 microgram to about 50 milligrams per inoculation (dose), preferably about 10 micrograms to about 10 milligrams per dose, most preferably about 100 micrograms to about 5 milligrams per dose.

[0108] Immunization can be conducted by conventional methods. For example, the immunogen can be used in a suitable diluent such as saline or water, or complete or incomplete adjuvants. Further, the immunogen may or may not be bound to a carrier. While it is possible for the immunogen to be administered in a pure or substantially pure form, it is preferable to present it as a pharmaceutical composition, formulation or preparation.

[0109] The formulations of the present invention, both for veterinary and for human use, comprise an immunogen as described above, together with one or more physiologically or pharmaceutically acceptable carriers and optionally other therapeutic ingredients. The carrier(s) must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not deleterious to the recipient thereof. The formulations may conveniently be presented in unit dosage form and may be prepared by any method well-known in the pharmaceutical art.

[0110] The immunogen can be administered by any route appropriate for antibody production such as intravenous, intraperitoneal, intramuscular, subcutaneous, and the like. The immunogen may be administered once or at periodic intervals until a significant titer of anti-sivrcm antibody is produced. The antibody may be detected in the serum using an immunoassay. The host serum or plasma may be collected following an appropriate time interval to prove a composition comprising antibodies reactive with the sivrcm virus particle or encoded polypeptide. The gamma globulin fraction or the igg antibodies can be obtained, for example, by use of saturated ammonium sulfate or DEAE Sephadex, or other techniques known to those skilled in the art.

[0111] In addition to its use to raise antibodies, the administration of the immunogens of the present invention may be for use as a vaccine for either a prophylactic or therapeutic purpose. When provided prophylactically, a vaccine(s) of the invention is provided in advance of any exposure to sivrcm or in advance of any symptoms due to sivrcm infection. The prophylactic administration of a vaccine(s) of the invention serves to prevent or attenuate any subsequent infection of sivrcm in a mammal. When provided therapeutically, a vaccine(s) of the invention is provided at (or shortly after) the onset of infection or at the onset of any symptom of infection or any disease or deleterious effects caused by sivrcm. The therapeutic administration of the vaccine(s) serves to attenuate the infection or disease. The vaccine(s) of the present invention may, thus, be provided either prior to the anticipated exposure to sivrcm or after the initiation of infection.

[0112] In another embodiment, the polypeptides of the invention can be used to prepare antibodies against sivrcm epitopes that are useful in diagnosis. The term “antibodies” is used herein to refer to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules. Exemplary antibody molecules are intact immunoglobulin molecules, substantially intact immunoglobulin molecules and portions of an immunoglobulin molecule, including those portions known in the art as Fab, Fab′, F(ab′)₂ and F(v) as well as chimeric antibody molecules.

[0113] An antibody of the present invention is typically produced by immunizing a mammal with an immunogen or vaccine of the invention. In one embodiment, the immunogen or vaccine contains one or more polypeptides of the invention, or a structurally and/or antigenically related molecule, to induce, in the mammal, antibody molecules having immunospecificity for the immunizing peptide or peptides. The peptide(s) or related molecule(s) may be monomeric, polymeric, conjugated to a carrier, and/or administered in the presence of an adjuvant. In another embodiment, the immunogen or vaccine contains one or more nucleic acids encoding one or more polypeptides of the invention, or one or more nucleic acids encoding structurally and/or antigenically related molecules, to induce, in the mammal, the production of the immunizing peptide or peptides. The antibody molecules may then be collected from the mammal if they are to be used in immunoassays or for providing passive immunity.

[0114] The antibody molecules of the present invention may be polyclonal or monoclonal. Monoclonal antibodies may be produced by methods known in the art. Portions of immunoglobulin molecules may also be produced by methods known in the art. The antibody of the present invention may be contained in various carriers or media, including blood, plasma, serum (e.g., Fractionated or unfractionated serum), hybridoma supernatants and the like. Alternatively, the antibody of the present invention is isolated to the extent desired by well known techniques such as, for example, by using DEAE SEPHADEX, or affinity chromatography. The antibodies may be purified so as to obtain specific classes or subclasses of antibody such as igm, igg, iga, igg₁, igg₂, igg₃, igg₄ and the like. Antibody of the igg class are preferred for purposes of passive protection.

[0115] The presence of the antibodies of the present invention, either polyclonal or monoclonal, can be determined by, but are not limited to, the various immunoassays described above. The antibodies of the present invention have a number of diagnostic and therapeutic uses. The antibodies can be used as an in vitro diagnostic agent to test for the presence of sivrcm in biological samples in standard immunoassay protocols. Preferably, the assays which use the antibodies to detect the presence of sivrcm in a sample involve contacting the sample with at least one of the antibodies under conditions which will allow the formation of an immunological complex between the antibody and the sivrcm antigen that may be present in the sample.

[0116] The formation of an immunological complex if any, indicating the presence of sivrcm in the sample, is then detected and measured by suitable means. Such assays include, but are not limited to, radioimmunoassays (RIA), ELISA, indirect immunofluorescence assay, Western blot and the like. The antibodies may be labeled or unlabeled depending on the type of assay used. Labels which may be coupled to the antibodies include those known in the art and include, but are not limited to, enzymes, radionucleotides, fluorogenic and chromogenic substrates, cofactors, biotin/avidin, colloidal gold and magnetic particles. Modification of the antibodies allows for coupling by any known means to carrier proteins or peptides or to known supports, for example, polystyrene or polyvinyl microtiter plates, glass tubes or glass beads and chromatographic supports, such as paper, cellulose and cellulose derivatives, and silica.

[0117] Such assays may be, for example, of direct format (where the labelled first antibody reacts with the antigen), an indirect format (where a labelled second antibody reacts with the first antibody), a competitive format (such as the addition of a labelled antigen), or a sandwich format (where both labelled and unlabelled antibody are utilized), as well as other formats described in the art. In one such assay, the biological sample is contacted with antibodies of the present invention and a labeled second antibody is used to detect the presence of sivrcm, to which the antibodies are bound.

[0118] The antibodies of the present invention are also useful as a means of enhancing the immune response. The antibodies may be administered with a physiologically or pharmaceutically acceptable carrier or vehicle therefor. A physiologically acceptable carrier is one that does not cause an adverse physical reaction upon administration and one in which the antibodies are sufficiently soluble and retain their activity to deliver a therapeutically effective amount of the compound. The therapeutically effective amount and method of administration of the antibodies may vary based on the individual patient, the indication being treated and other criteria evident to one of ordinary skill in the art. A therapeutically effective amount of the antibodies is one sufficient to reduce the level of infection by one or more of the viruses of this invention or attenuate any dysfunction caused by viral infection without causing significant side effects such as non-specific T cell lysis or organ damage.

[0119] The route(s) of administration useful in a particular application are apparent to one or ordinary skill in the art. Routes of administration of the antibodies include, but are not limited to, parenteral, and direct injection into an affected site. Parenteral routes of administration include but are not limited to intravenous, intramuscular, intraperitoneal and subcutaneous.

[0120] The present invention includes compositions of the antibodies described above, suitable for parenteral administration including, but not limited to, pharmaceutically acceptable sterile isotonic solutions. Such solutions include, but are not limited to, saline and phosphate buffered saline for intravenous, intramuscular, intraperitoneal, or subcutaneous injection, or direct injection into a joint or other area.

[0121] Antibodies for use to elicit passive immunity in humans are preferably obtained from other humans previously inoculated with pharmaceutical compositions comprising one or more of the polypeptides of the invention. Alternatively, antibodies derived from other species may also be used. Such antibodies used in therapeutics suffer from several drawbacks such as a limited half-life and propensity to elicit an immune response. Several methods are available to overcome these drawbacks. Antibodies made by these methods are encompassed by the present invention and are included herein. One such method is the “humanizing” of non-human antibodies by cloning the gene segment encoding the antigen binding region of the antibody to the human gene segments encoding the remainder of the antibody. Only the binding region of the antibody is thus recognized as foreign and is much less likely to cause an immune response.

[0122] In providing the antibodies of the present invention to a recipient mammal, preferably a human, the dosage of administered antibodies will vary depending upon such factors as the mammal's age, weight, height, sex, general medical condition, previous medical history and the like. In general, it is desirable to provide the recipient with a dosage of antibodies which is in the range of from about 5 mg/kg to about 20 mg/kg body weight of the mammal, although a lower or higher dose may be administered. In general, the antibodies will be administered intravenously (IV) or intramuscularly (IM).

[0123] The invention also relates to the use of antisense nucleic acids to inhibit translation of peptides encoded by sivrcm. The antisense nucleic acids are complementary to sivrcm mrnas encoding peptides of this invention. The antisense nucleic acids may be in the form of synthetic nucleic acids or they may be encoded by a nucleotide construct, or they may be semi-synthetic. The antisense nucleic acids may be delivered to the cells using methods known to those skilled in the art.

[0124] Kits designed for diagnosis of sivrcm in a biological sample can be constructed by packaging the appropriate materials, including the nucleic acids and/or polypeptides of this invention and/or antibodies which specifically react with sivrcm antigens, along with other reagents and materials required for the particular assay. The following examples illustrate certain embodiments of the present invention, but should not be construed as limiting its scope in any way. Certain modifications and variations will be apparent to those skilled in the art from the teachings of the forgoing disclosure and the following examples, and these are intended to be encompassed by the spirit and scope of the invention.

EXAMPLE 1

[0125] PCR Amplification, Molecular Cloning and Sequence Analysis of the Sivrcm Genome

[0126] We have PCR amplified, cloned, and sequenced a complete sivrcm proviral genome from a short-term PBMC culture originally established from the blood of a Gabonese red capped mangabey (82). Because of the extensive genetic diversity of this new SIV strain, we had to devise a novel PCR strategy to derive its genome. First, we amplified two small fragments in gag and pol, using primers corresponding to sequences highly conserved among all known primate lentiviral lineages. This allowed us to subsequently design strain-specific primers to amplify the region between gag and pol (gag/pol) as well as the regions outside (flanking) gag and pol by placing the primers in reverse and amplifying the rest of the genome from unintegrated circular DNA molecules. Strategy and primer pairs are shown in FIG. 1. Overlapping PCR fragments were sequenced in their entirety.

[0127] Sequence analysis of the entire provirus revealed a genomic organization previously found only in members of the HIV-2/sivsm/sivmac group of viruses. That is, in addition to gag, pol, vif, vpr, env, tat, rev and nef genes, sivrcm also encoded a vpx homologue thus far only been found in members of the HIV-2/sivsm/sivmac lineage (FIG. 3). Moreover, secondary structure analysis of its LTR sequences revealed a duplicated TAR stemloop structure, again a signature of sivsm/sivmac/HIV-2 viruses (FIG. 4). Based on these findings, we expected sivrcm to fall within a greater mangabey lineage, forming a distinct subcluster similar to what has been observed for the four species-specific subclusters of sivagm.

[0128] However, phylogenetic analyses failed to identify such a relationship of sivrcm with the HIV-2/sivsm/sivmac group (FIG. 5). Instead of grouping closely with other mangabey viruses, sivrcm clustered independently in most regions of its genome, forming a sixth lineage roughly equidistant from the other viruses (FIG. 5). In env and nef, sivsm, sivrcm and sivagm viruses appeared to be relatively more closely related to each other than they were to sivcpz, sivsyk and sivmnd; however, even in these regions there was no particularly close relationship between the two mangabey lineages (FIGS. 5C and 5D). Also, in trees derived from the 3′ and 5′ pol regions, sivrcm clustered with HIV-1 and sivcpz viruses, with significant bootstrap values (FIG. 5B). Finally, there was also a close relationship between sivrcm and sivagmsab, a virus we have previously reported to be mosaic with a divergent mangabey lineage in the 5′ half of its genome (21). In the 5′ half of gag, these two viruses clustered with significant bootstrap values (FIG. 5A), indicating that sivrcm likely represents this previously hypothesized divergent mangabey lineage. These results were confirmed by the use of maximum likelihood approaches to determine tree topologies.

[0129] The results suggest that sivrcm represents a highly divergent mangabey virus which forms an independent lineage (for most of its genome) roughly equidistant from all other primate lentiviruses. The extent of diversity between sivrcm and the other mangabey lineage (sivsm) is surprising, given the known relationships of sivagm strains from different African green monkey species. One explanation for this is that mangabeys acquired their SIV infection a very long time ago (millions of years), even before African green monkeys became infected with sivagm. Another is that these viruses have evolved with in their respective species with vastly different rates of evolution. Also of interest are the close phylogenetic relationships of sivrcm to sivcpz in the 3′ and 5′ pol regions, as well as to sivagmsab in the gag region, which are highly significant. These finding strongly suggest recombination events in the distant past. However, based on current data it is impossible to determine which of these lineages are mosaic. For example, it is quite conceivable the sivrcm is non-recombinant and that both sivcpz and sivagmsab viruses acquired sivrcm sequences independently through cross-species transmission events in the past. This would also mean that HIV-1 is mosaic with sivrcm related sequences. These findings are important because they indicate that primate lentiviral evolution is far more complex than previously appreciated, and that sequences from additional primate lentiviruses (in particular sivcpz, sivrcm, and sivagm strains from Gabon and Cameroon) are critically needed to resolve the unexpected phylogenetic relationships of sivrcm.

EXAMPLE 2

[0130] Identification of a New Reading Frame in Sivrcm and Sivsm Viruses

[0131] Analysis of the sivrcm sequence revealed that there were about 100 bp of “non-coding sequences” between the splice donor site of the first tat and rev exons, and the initiation codon of the env open reading frame (ORF). Upon closer analysis, it was realized that the first exon of rev, instead of being terminated by a stop codon immediately downstream of the splice site, continued uninterrupted for about 100 more base pairs. Comparison of the genomic organization of members of all other major primate lentiviral lineages indicated that there was only one other group, i.e., The sivsm/sivmac group, that had a similarly “extended first rev exon”. All other viruses had stop codons shortly after the splice site (except for members of the HIV-1/sivcpz group, which encode the vpu gene in this region).

[0132]FIG. 6 shows an alignment of the deduced amino acid sequence of the sivsmpbj1.9 and sivrcmgb1 extended rev orfs. The putative pbj protein is 71 amino acids in length, while the putative sivrcm protein is shorter, i.e., Only 54 amino acids. However, this shorter length could be the result of inactivating mutations (frameshift and in frame stop codons). Assuming a “corrected” sequence, the sivrcm extended rev ORF would encode a 105 amino acid protein (FIG. 6) with considerable sequence homology to the corresponding sivsm product throughout its entire length. Correction of inactivating mutations would restore the predicted coding capacity of the sivrcm rev ORF to a protein of 105 amino acids, and nucleic acids containing repaired coding sequences, as well as the polypeptides encoded by the repaired coding sequences, are also considered to be a part of the invention.

[0133] The conservation of the extended rev orfs among different members of the HIV-2/sivsm/sivmac group of virus was also examined. FIG. 7 shows an amino acid sequence alignment, including all sequences from the Los Alamos HIV sequence database. The results were surprising: all sivsm/sivmac strains encoded a highly conserved and uninterrupted open reading frame; however, all HIV-2 strains, except one (FO784) which we was considered to represent an ill-adapted sooty managbey virus in humans, contained inactivating mutations (stop codons) in this “extended rev ORF”.

[0134] The finding of an “extended rev first exon ORF” in both sivrcm and sivsm lineages is significant for several reasons: (i) it suggests the existence of a “mangabey virus specific” protein, which likely plays an important role in mangabey virus replication (as do all other accessory proteins); (ii) it suggests the existence of a “mangabey virus specific” protein whose expression may be abrogated as a consequence of sivsm adaptation to the human host; (iii) it suggests the existence of a “managbey virus specific” protein, which could serve as a functional vpu equivalent (the position of this new ORF in the sivrcm/sivsm genome, as well as its overall length, are reminiscent of the vpu gene in HIV-1/sivcpz, although amino acid sequence homologies between the putative sivsm/sivrcm extended first rev exon product and the HIV-1/sivcpz Vpu protein were not found; however, this is not necessarily surprising since the Vpu proteins among different members of the HIV-1/sivcpz lineage are so divergent that they cannot be aligned (52). These findings are important for the current application because they highlight another potential structural similarity between sivrcm and sivsm lineages. However, additional sivrcm isolates need to be characterized to confirm the existence of this reading frame (and its putative protein product) among other viruses.

[0135] The following references are cited herein:

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[0218] Modification of the above described invention that are obvious to those of skill in the fields of genetic engineering, immunology, protein chemistry, medicine, and related fields are intended to be within the scope of the following claims. All of the references cited herein above are hereby incorporated by reference.

1 58 1 9465 DNA Simian immunodeficiency virus Nucleotide sequence of the SIVrcm genome 1 tggcgcccga acagggactt gagagtggct gagagacctc cgaggctaag gttcggcgcg 60 gcaggtcacc gcgggagtgg aaccttgacc aggtaagagc tgcctggtgg cttcaaagtg 120 ctagagaaag tgagctagcg aaggaagcag ggcaacccgg tccggtactg ggcctctagg 180 gaaggagcga agtcctagag aagggaggaa aatgggtgcg agagcctcat tgttgtcagg 240 gaagaagcta gacgcatggg aatcagttag gttacggccc ggcgggaaaa agaaatacat 300 gctgaagcat ttggtatggg catgcaaaaa actaaataaa tttggcttga gtgatcattt 360 gttagaaaca gcaacaggat gtgaaaaaat attaggagtc ctgctgcctc tagttccgac 420 agggtcagag gggctaaaaa gcctctttaa tttgtgctgc gtactctggt gcgtacacaa 480 ggaagtgaaa gtgaaagaca cagaggaagc tgtagcaaaa gtgaaagaat gctgccatct 540 agtggaaaaa gcagaaaata caacagaaaa agaaaaggga gcaacagcgc cacctagtgg 600 acaaagagga aattatccta taattactat aaatcagcag cctgagcata atcctatatc 660 accaaggact ctaaatgcct gggtcaaggt ggtagaggag aaaaaattct cagcagaagt 720 agcgcccatg ttctcggcac tatcagaagg ctgcataccc tatgatataa atcaaatgct 780 aaatgccata ggggaacacc agggtgcgct gcagatagta aaggaagtga tcaatgagga 840 agcagcagac tgggatgcta gacatccagt accaggcccg ataccagcag ggcaacttag 900 agaaccaaca ggaagtgaca tagcagggac aactagctca atagcagaac agatagcttg 960 gaccaccaga gcaaacaacc ccattaatgt gggcaatctg tacagaaatt ggataatagt 1020 agggttacaa aaatgggtaa aaatgtacaa tccagtgaac atcctagata taaagcaagg 1080 accaaaagag tcattcaagg attatgtgga tagattttat aaagccttga gagcagaaca 1140 ggcagacccg gcagtaaaaa attggatgac acaatcactg ctgatacaaa atgctaaccc 1200 agactgtaaa atggtactca agggtctggg aatgaaccct tctttagaag aaatgctaac 1260 agcctgtcag ggggtaggag gaccccagca taaagctcgg gtactagcag aggccatgca 1320 aatgatgcaa agtaatatca tggctcagca atcagcaaac agggggcctc caagaagatc 1380 aggaggaaat ccaaatttaa gatgttacaa ttgtggtaag ccaggacaca tttctagata 1440 ttgtaaagcc cctagaagga agggatgctg gaaatgtgga tccccagacc atctcttgaa 1500 agactgcaca aagcaaataa attttttagg gagactcccc tggggtcagg ggaagccgag 1560 gaactttcct ttgacttcct tgactccctc tgctccaggg atggagagca attacgaccc 1620 tgcagaagag atgctaaaga attatctgag gagggcaggg gaacaaaaga gacaacagag 1680 gcaggaagag agcaagaaga gagagggagc atatcaggaa gccttaacct ccctcaattc 1740 gctctttgga agcgaccaac tacaatagct caaatagaag ggcagaaagt ggaggtccta 1800 ttagacacag gagcagatga cacagtaatt gaaggaatag aattaggaaa tgattggacc 1860 ccaaaaataa taggaggaat agggggatat attaatgtaa aacaatataa aaactgtgaa 1920 attgaaatag ctggaaaaag gactcatgct catgtgctag tgggaccaac accagtgaat 1980 attataggga gaaatgtttt aaagaaatta ggagccacac taaattttcc aataagccaa 2040 atagaaacta taaaggtaga attaaagtct ggacaagatg gaccacgagt aaaacaatgg 2100 ccattgtcaa aagaaaaaat agaagcttta acagaaattt gcaatgcaat ggagaaggaa 2160 ggaaaaattt caaaaatagg gccagaaaac ccctacaaca caccaatatt ctgtattaaa 2220 aagaaagact ccacaaaatg gagaaaattg gtagatttta gagaactaaa taagagaaca 2280 caggactttt ttgaggtgca gctgggaata ccacatccag gaggattaaa gcaatgtgag 2340 agaataacgg tattagacat cggggatgca tatttttcat gtcttctgta tgagcctttt 2400 aggaaatata ctgcatttac aataccagca gtaaataatc aaggaccagg agtgaggtat 2460 caatataatg tgctgcctca gggatggaag ggatctcccg ccatctttca ggcatcagcc 2520 aataagatct tacagccatt tagggaagag aatccagatg tcatcattta ccagtacatg 2580 gatgatctct ttgtaggctc agatagaaca aagttggaac atgacaaaat gatcaaacaa 2640 ttaagagatc atctactgtt ctggggcttt gagaccccag acaaaaaatt tcaggataaa 2700 cctccatatt tgtggatggg gtatgagctg cacccaaaaa gttggacagt acaggagatc 2760 aagttaccag agaaagaaga atggacagtt aacgatattc agaaattagt aggaaagtta 2820 aactgggcaa gtcaaattta cagtgggcta aggactaagg aattgtgcaa gttgataagg 2880 ggagcaaaag cattagatga aaaagtagaa atgacaaaag aagcagaaat agaatatgaa 2940 gaaaacaaga tgattctaaa agaaaagttg catggggtgt attatgatga aaagaaaccc 3000 ttagtggcaa acattcagaa gttagaaggt ggacagtggt cctatcaaat agaacaggag 3060 tcaggaaaac cactgaaaac aggcaaatat gctaagcaga aaacagcaca caccaatgaa 3120 attagaatgc tggcagggtt agtacaaaaa attgcaaaag aagccatagt tatttgggga 3180 aggctgccaa cattcagact gccaatagag agagaggtat gggactaatg gcggtcccaa 3240 tactggcagg ttacctggat accagattgg gaatttgtta gcacaccacc tcttattaga 3300 ctcgggtaca acctagttaa ggatcccata ccaggagagg aagtctacta tgtggatggg 3360 gcagctaaca gaaatagtaa aataggaaag gcgggatatg ttacaaatag aggaaaagaa 3420 aaggtaaaag aattagaaga aactactaat caaaaagcag aattagaagc agtattactg 3480 gcattaaaag attcagggcc taaagtaaac atagtcacag attcacagta tgtttatgga 3540 attctagaag cacaaccaga tactagtgac tcagggttag tgacagaaat tataaatcag 3600 atgataggga aagaagcagt gtacctttcc tgggtgcccg cacataaggg catcggagga 3660 aatgaggaag tagataaatt agttagtaaa ggaatcagac aggtactgtt cctagatggg 3720 atagaaaaag cacaagaaga acatgaaaag tatcataata attggagagc attggcagaa 3780 gattttcaaa ttccacaaat agtggcaaaa gaaatagtag cacagtgtcc aaaatgtcaa 3840 gtaaaagggg aagcaatcca tgggcaagtg gatgcaagtc cagggacttg gcaaatggac 3900 tgcacacatt tggaaggaaa aataatcata gtagcagtcc atgtggcaag tggatatata 3960 gaggcagaag taataccagc agaaacagga aaagagacag cacatttcct gttgaaacta 4020 gcagcaagat ggccagtaag gaagctacac acagataatg gagcaaattt cacaagtgca 4080 gcagtacagg cggtctgctg gtgggctcag atagagcacg cctttggagt accttacaat 4140 cctcaaagtc aaggagtagt ggaaagcatg aataaacaat taaaaataat catagaacaa 4200 gtaagagaac aagcagaaaa attagaaaca gcagtccaaa tggcagtttt ggttcacaat 4260 tttaaaagaa aaggggggat tggggggtac agtgcaggag aaagaataat agatataata 4320 gcaacagact tagcaaccaa taaattacaa aatcaaattt caaaaattca aaattttcgg 4380 gtttattaca gagaaggaag ggatcaactg tggagaggtc cagctaagct gatctggaaa 4440 ggagaaggag cagtagtcat ccaggaggag actggagact tgaaggtagt ccccaggaga 4500 aaagcaaaaa tcataaaaga atatggcaga aaagatgtgg atagtgaggc caatttggcg 4560 ggtagacagg aggaaaattg aacaatggca ctctttggta aaatatcatc agtacaaagg 4620 aaagaaagca gcaaaagagt gggagtatgt gcctcacttt aaagtaccat ggggatggtg 4680 gtcgcattca gaagttcaca tacctttaga ggaaggatca aagttaaaaa taaccaccta 4740 ttggaatttg acagtagaaa agggatggct agggacatat ggggtaggaa tcttatggat 4800 aaaaggagat tatgtaacag atgtatttcc ttggactgca gatagtttaa tacataaaat 4860 ttattttcca tgttttacag atagagcaat cagacaaagt ctactagggg aaaaagttct 4920 agtgtgtgcc ttccaagggg gacatagaga tcaggtaggg actctgcaat ttttggcaat 4980 acaagcgtgg gctaaaagtc agttagatag gtatggcaga aagagccccc gaggtcccca 5040 ctggggctgg agaagcagag ttccagcctt ggctacggga catgctagaa aaggtcaact 5100 tggaagccag gttacacttt catccagagt tcattttccg tctgtggcgc acttgtgtgg 5160 aacactggca tgacgtacat cagagaagtt tagaatatgc tgcttatagg tacttactgc 5220 tgatgcaaaa ggctttgttt atccactgtc agacagggtg tagtcagaga catggaccca 5280 atcctagggc agtaggagaa aggataacca tcctaccggg gatgtaatga tggccctctc 5340 tttacagaga tggagctgcc ccctgaggat gaaggtccgc aacgagaacc ttatgatgaa 5400 tggttaatgg ataccctaat agagttgcaa gaagaagcta agaaacattt tacatatgct 5460 ttgctaacgc aaataggaga ttatgtatat gagcaacatg gggatagcat agagggagtg 5520 caggcaatga ttcggctgct tcaaagagcc ttgtttcttc attttagaaa tggatgtgca 5580 gggagtagga ttggaacatc cagaggaagt aatcctctac gatccattcc gcaaacgaga 5640 aacatcatgt aacacttgtt attgtaaaaa atgttgttat cactgccaac tctgcttcct 5700 gcagaaagga ctaggcataa attatgcttc cagggcaaga cgaagaagat ctaaggaaga 5760 aaataaggct gataaatttc ctgtacctaa tcagtaagta tggagtgccc tggactagta 5820 ctgcttttag agcctcagct aaaaaggttt ttatagatct tttagttaca ataattaaag 5880 gaaaatagaa taagataaga tggataagaa attagtaata gtattaatag tagtaatagg 5940 gataatacta gtacaaggat cacaaaaacc gcaatatata acagtcttct atggtgtccc 6000 agtatggaga aacagcacag tgcctatgtt ttgtgtgact gataatactc aatcatgggg 6060 aactctaaat tgtataccag agggaggaat atctccagag gtttcaataa atgtgtcaga 6120 acgatttgat gcttggaata atagcttata tgaacaagca aaagataatg tgtggaatct 6180 ttatgattcc actctaaaac catgtgtcag attaagccca ttatgtatta ccatgaattg 6240 ttcagcaata aatggtagct gggatggaat ccctacctca gcaccaccaa caacaacaaa 6300 aacaacaaca caaagaacta taggtgtaga aaaggaatgt actgctggca acgaaacatg 6360 tgaggaagtt caggatgcag atgtgatgtc ttgtgaattt gctgtagcag gactaaagag 6420 agatgagaaa cacaagtata atgatacctg gtattctaga gacctttggt gtgaaaagga 6480 aacaaattct acaaattcta caaaaaagaa atgttttgta aggcactgca atacaacttc 6540 catacaacaa ttttgtgaac caaagtactg ggaaccattt aggttaagat attgtgctcc 6600 accagggttt gccttactgg tctgcaaaga taaaaattat acaggctttg atacctgtgt 6660 taatgttact gccacttcat gcacacatat gattaatact actgtggcct cagggtttgg 6720 attaaatgga tcaattaatg taaatgagac ttggatatat cagagaaggc aaagtaatag 6780 gacagttata ggtctcaata gtttttataa tttgtcagta acatgcagga gaccttcaaa 6840 tagaacagtg aaagggatat cgctagcaac aggagtcttt atctcactaa gagtagagaa 6900 gagaccaaaa ggagcttggt gtagatttga agggaattgg acggatgcat ggaaagaagt 6960 aaaagagaga gtgaaaacaa caaaagggta tcgaggtact agtaacacag acaaaataaa 7020 gataagaaca gtatatggtg gagatgatga ggcaagatat ttctggctaa attgtaatgg 7080 agaattttta tattgcaagt taaattggtt tttaaatttg ttaaataatg agacagtagg 7140 gacaacaaat gagaagagaa aagcaccttt tgtaccatgc atcacaaaaa tgatagtcaa 7200 tgattggtat acagtatcga ggaaggtata cacgccaccg aggccagatg cgttaaagtg 7260 cagtgcacag gtatcctatc tgttggcaga catagactat attaatgaca gtgagacaaa 7320 catcaccctc tcagcggaag tgggtgatta ttgggcagca gaattgggga gatataaggc 7380 aatagaaatc agaccaattg gctttgcacc aacagaaata aaaaggtacc agacgaaaca 7440 gaaaagggta cctttggtgc tgggttttct aggtttcctc tcagcagcag gtactgcaat 7500 gggcgcagcg gcgacagccc tgactgtcca gtcccggcat ttgcttgcag ggatattgca 7560 gcagcaaaag aacctgctgg acatagttaa gcggcagcag aatctgctaa agctcaccgt 7620 ctggggaact aaaaatctcc aggcgcgtgt cactgctatt gagaaatacc tagcagacca 7680 atctctattg aatacatttg ggtgtgcctg gagacaagtc tgccatacag tggtgccgtg 7740 gacattcaac aaaacgcctg agtggcagaa agaatcatgg ttgcagtggg aaagaaatat 7800 ctcttattta gaggctaaca ttacaatagc attacaggag gcccaggatc aacatgagaa 7860 aaatgtgcat gaattggaga aattaagtaa ttggggagat gcattcagtt ggctgaatct 7920 tgactggtgg atgcaatata taaaaatagg cttctttata gtaataggta tcataggatt 7980 aagagtagct tggctgttat ggaattgtct tagtaatctt aggcaagggt ataggcctct 8040 ctccccaccc tcttatgttc agcagatcca tatccacaac acgggggaac cgcaaactcc 8100 aggagaaaaa agagaagacg gtggagaaga aggtggcaac aagtacaaca attggctgag 8160 agaatattgc tggattcaac tgatccaccc gttgagcagg atttggacgc agctatcgca 8220 gatttgcaga agctgcagct caataatctt ccagagcctc cggtggattt tagctaagat 8280 acaatatggg tggcaagagt tcaaagaatt cagcagctgg tttgctgaga tggcgcttca 8340 aaatgcttac tacacctgga gagggttatg tgcggtggca cgagactttg ctggatggcc 8400 agccatggtg tgcagaagga tcaggcaggg cctcgagaga ctttgtaatt agaggaggca 8460 ttacagcaga aacgcaagct tcaatagatg acattgactg gtatgaagat actgatgaca 8520 ccttggtagg atttccagtg aaacctcaag taccacttag accaatgagt tacaagctag 8580 caatagacat gtctcacttt ttaaaagaaa aggggggact ggaagggatt tattggagta 8640 tcagaagaca aagaatattg gatatgtacc tggaaaatga gcatggcata atacctgatt 8700 ggcaaaacta cactccaggg ccaggaataa gatatccaac actgtttgga tggctctggc 8760 aattggtgcc agtagatgta tctgatgaag caagagaaga tgaagagcat agtttgctac 8820 atccagcaga aacaagtggg atggaagacc catgggggga ggtcttggcc tggaagttta 8880 atcctatgct ggcagtagat tacataggct atagactgca tccagagttc tttggggaaa 8940 ggaagaacaa gacccagtaa ccacatcctc tggggttgcc ttggtaacca ggcagaagaa 9000 tctgctgatg caaaagggac tttccactgg tgcatgcgca ctggggaagg gactttccgg 9060 gatgacgtgg gagggggagt ggtcagccct ctcctgctgc atataagcag ctgctctgcg 9120 cttgtaaaac gggtctctcc ctgggaggct accggattga gcctgggtgt tctctggtaa 9180 gtctctagga actccagctt gagcctgggt gttcgctggt gtctctgaac aggcttgctg 9240 gggtgcctct cgctcttcgg gtagaccgcc agttgaggct cggccggcct caacgggaga 9300 gatcaccgct tgcttatagc cttgaagctc aataaagcat gccagttagt ttactgtaag 9360 caagtgtgtg cctgttttac ctctcagcag ttaacgactc tggggtaggg atccctcaga 9420 ttcttgtggc agaagagcct tgggctaaga aaattcccta ccagt 9465 2 25 DNA Simian immunodeficiency virus Gag A primer 2 aggttacggc ccggcggaaa gaaaa 25 3 32 DNA Simian immunodeficiency virus Gag B primer 3 cctactccct gacaggccgt cagcatttct tc 32 4 28 DNA Simian immunodeficiency virus Gag 1 primer 4 ttagagaacc aacaggaagt cacatagc 28 5 25 DNA Simian immunodeficiency virus Gag 2 primer 5 tccacagttg atcccttcct tctct 25 6 23 DNA Simian immunodeficiency virus Gag r1 primer 6 tcggaactag aggcagcagg act 23 7 25 DNA Simian immunodeficiency virus Gag r2 primer 7 ctagcagcaa gatggccagt aagga 25 8 23 DNA Simian immunodeficiency virus UNIPOL1 primer 8 agtggattca tagaagcaga agt 23 9 19 DNA Simian immunodeficiency virus SS2 primer 9 tactgcccct tcacctttc 19 10 850 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of SIVrcm lentiviral env protein 10 Met Asp Lys Lys Leu Val Ile Val Leu Ile Val Val Ile Gly Ile Ile 1 5 10 15 Leu Val Gln Gly Ser Gln Lys Pro Gln Tyr Ile Thr Val Phe Tyr Gly 20 25 30 Val Pro Val Trp Arg Asn Ser Thr Val Pro Met Phe Cys Val Thr Asp 35 40 45 Asn Thr Gln Ser Trp Gly Thr Leu Asn Cys Ile Pro Glu Gly Gly Ile 50 55 60 Ser Pro Glu Val Ser Ile Asn Val Ser Glu Arg Phe Asp Ala Trp Asn 65 70 75 80 Asn Ser Leu Tyr Glu Gln Ala Lys Asp Asn Val Trp Asn Leu Tyr Asp 85 90 95 Ser Thr Leu Lys Pro Cys Val Arg Leu Ser Pro Leu Cys Ile Thr Met 100 105 110 Asn Cys Ser Ala Ile Asn Gly Ser Trp Asp Gly Ile Pro Thr Ser Ala 115 120 125 Pro Pro Thr Thr Thr Lys Thr Thr Thr Gln Arg Thr Ile Gly Val Glu 130 135 140 Lys Glu Cys Thr Ala Gly Asn Glu Thr Cys Glu Glu Val Gln Asp Ala 145 150 155 160 Asp Val Met Ser Cys Glu Phe Ala Val Ala Gly Leu Lys Arg Asp Glu 165 170 175 Lys His Lys Tyr Asn Asp Thr Trp Tyr Ser Arg Asp Leu Trp Cys Glu 180 185 190 Lys Glu Thr Asn Ser Thr Asn Ser Thr Lys Lys Lys Cys Phe Val Arg 195 200 205 His Cys Asn Thr Thr Ser Ile Gln Gln Phe Cys Glu Pro Lys Tyr Trp 210 215 220 Glu Pro Phe Arg Leu Arg Tyr Cys Ala Pro Pro Gly Phe Ala Leu Leu 225 230 235 240 Val Cys Lys Asp Lys Asn Tyr Thr Gly Phe Asp Thr Cys Val Asn Val 245 250 255 Thr Ala Thr Ser Cys Thr His Met Ile Asn Thr Thr Val Ala Ser Gly 260 265 270 Phe Gly Leu Asn Gly Ser Ile Asn Val Asn Glu Thr Trp Ile Tyr Gln 275 280 285 Arg Arg Gln Ser Asn Arg Thr Val Ile Gly Leu Asn Ser Phe Tyr Asn 290 295 300 Leu Ser Val Thr Cys Arg Arg Pro Ser Asn Arg Thr Val Lys Gly Ile 305 310 315 320 Ser Leu Ala Thr Gly Val Phe Ile Ser Leu Arg Val Glu Lys Arg Pro 325 330 335 Lys Gly Ala Trp Cys Arg Phe Glu Gly Asn Trp Thr Asp Ala Trp Lys 340 345 350 Glu Val Lys Glu Arg Val Lys Thr Thr Lys Gly Tyr Arg Gly Thr Ser 355 360 365 Asn Thr Asp Lys Ile Lys Ile Arg Thr Val Tyr Gly Gly Asp Asp Glu 370 375 380 Ala Arg Tyr Phe Trp Leu Asn Cys Asn Gly Glu Phe Leu Tyr Cys Lys 385 390 395 400 Leu Asn Trp Phe Leu Asn Leu Leu Asn Asn Glu Thr Val Gly Thr Thr 405 410 415 Asn Glu Lys Arg Lys Ala Pro Phe Val Pro Cys Ile Thr Lys Met Ile 420 425 430 Val Asn Asp Trp Tyr Thr Val Ser Arg Lys Val Tyr Thr Pro Pro Arg 435 440 445 Pro Asp Ala Leu Lys Cys Ser Ala Gln Val Ser Tyr Leu Leu Ala Asp 450 455 460 Ile Asp Tyr Ile Asn Asp Ser Glu Thr Asn Ile Thr Leu Ser Ala Glu 465 470 475 480 Val Gly Asp Tyr Trp Ala Ala Glu Leu Gly Arg Tyr Lys Ala Ile Glu 485 490 495 Ile Arg Pro Ile Gly Phe Ala Pro Thr Glu Ile Lys Arg Tyr Gln Thr 500 505 510 Lys Gln Lys Arg Val Pro Leu Val Leu Gly Phe Leu Gly Phe Leu Ser 515 520 525 Ala Ala Gly Thr Ala Met Gly Ala Ala Ala Thr Ala Leu Thr Val Gln 530 535 540 Ser Arg His Leu Leu Ala Gly Ile Leu Gln Gln Gln Lys Asn Leu Leu 545 550 555 560 Asp Ile Val Lys Arg Gln Gln Asn Leu Leu Lys Leu Thr Val Trp Gly 565 570 575 Thr Lys Asn Leu Gln Ala Arg Val Thr Ala Ile Glu Lys Tyr Leu Ala 580 585 590 Asp Gln Ser Leu Leu Asn Thr Phe Gly Cys Ala Trp Arg Gln Val Cys 595 600 605 His Thr Val Val Pro Trp Thr Phe Asn Lys Thr Pro Glu Trp Gln Lys 610 615 620 Glu Ser Trp Leu Gln Trp Glu Arg Asn Ile Ser Tyr Leu Glu Ala Asn 625 630 635 640 Ile Thr Ile Ala Leu Gln Glu Ala Gln Asp Gln His Glu Lys Asn Val 645 650 655 His Glu Leu Glu Lys Leu Ser Asn Trp Gly Asp Ala Phe Ser Trp Leu 660 665 670 Asn Leu Asp Trp Trp Met Gln Tyr Ile Lys Ile Gly Phe Phe Ile Val 675 680 685 Ile Gly Ile Ile Gly Leu Arg Val Ala Trp Leu Leu Trp Asn Cys Leu 690 695 700 Ser Asn Leu Arg Gln Gly Tyr Arg Pro Leu Ser Pro Pro Ser Tyr Val 705 710 715 720 Gln Gln Ile His Ile His Asn Thr Gly Glu Pro Gln Thr Pro Gly Glu 725 730 735 Lys Arg Glu Asp Gly Gly Glu Glu Gly Gly Asn Lys Tyr Asn Asn Trp 740 745 750 Leu Arg Glu Tyr Cys Trp Ile Gln Leu Ile His Pro Leu Ser Arg Ile 755 760 765 Trp Thr Gln Leu Ser Gln Ile Cys Arg Ser Cys Ser Ser Ile Ile Phe 770 775 780 Gln Ser Leu Arg Trp Ile Leu Ala Lys Ile Gln Tyr Gly Trp Gln Glu 785 790 795 800 Phe Lys Glu Phe Ser Ser Trp Phe Ala Glu Met Ala Leu Gln Asn Ala 805 810 815 Tyr Tyr Thr Trp Arg Gly Leu Cys Ala Val Ala Arg Asp Phe Ala Gly 820 825 830 Trp Pro Ala Met Val Cys Arg Arg Ile Arg Gln Gly Leu Glu Arg Leu 835 840 845 Cys Asn 850 11 855 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of A_U455 lentiviral env protein 11 Met Arg Val Met Gly Ile Gln Arg Asn Tyr Pro Cys Leu Trp Arg Trp 1 5 10 15 Gly Thr Met Ile Leu Gly Leu Ile Ile Ile Cys Asn Ala Gln Gln Leu 20 25 30 Trp Val Thr Val Tyr Tyr Gly Val Pro Val Trp Lys Asp Ala Val Thr 35 40 45 Thr Leu Phe Cys Ala Ser Asp Ala Lys Ala Tyr Asp Ala Glu Val His 50 55 60 Asn Val Trp Ala Thr His Ala Cys Val Pro Thr Asp Pro Asn Pro Gln 65 70 75 80 Glu Ile Asp Leu Val Asn Val Thr Glu Glu Phe Asn Met Trp Lys Asn 85 90 95 Asn Met Val Asp Gln Met His Glu Asp Ile Ile Ser Leu Trp Asp Gln 100 105 110 Ser Leu Lys Pro Cys Val Lys Leu Thr Pro Leu Cys Val Thr Leu Asp 115 120 125 Cys His Asn Ile Thr Ile Asn Asn Thr Asn Asn Asn Thr Asn Ile Thr 130 135 140 Asp Gly Val Arg Glu Glu Met Lys Asn Cys Ser Phe Asn Met Thr Thr 145 150 155 160 Glu Leu Arg Asp Lys Lys Gln Lys Val Tyr Ser Leu Phe Tyr Arg Leu 165 170 175 Asp Ile Val Gln Ile Asn Lys Thr Asp Asn Asn Ser Tyr Arg Leu Ile 180 185 190 Asn Cys Asn Thr Ser Thr Ile Thr Gln Ala Cys Pro Lys Val Ser Phe 195 200 205 Glu Pro Ile Pro Ile His Tyr Cys Ala Pro Ala Gly Phe Ala Ile Leu 210 215 220 Lys Cys Lys Asp Pro Glu Phe Asn Gly Lys Gly Pro Cys Arg Asn Val 225 230 235 240 Ser Thr Val Gln Cys Thr His Gly Ile Lys Pro Val Val Ser Thr Gln 245 250 255 Leu Leu Leu Asn Gly Ser Leu Ala Glu Arg Glu Ile Arg Ile Arg Ser 260 265 270 Glu Asn Phe Thr Asn Asn Ala Lys Thr Ile Ile Val Gln Leu Val Asn 275 280 285 Pro Val Lys Ile Asn Cys Ser Arg Pro Tyr Asn Thr Arg Lys Asn Ile 290 295 300 Arg Arg Tyr Ser Ile Gly Ser Gly Gln Ala Phe Tyr Val Thr Gly Lys 305 310 315 320 Ile Ile Gly Asp Ile Arg Gln Ala His Cys Asn Val Ser Arg Arg Asp 325 330 335 Trp Asn Arg Thr Ile Gln Gln Val Ala Glu Gln Leu Lys Lys Lys Phe 340 345 350 Asn Asn Lys Thr Ile Ile Phe Ala Ser Ser Ser Gly Gly Asp Ile Glu 355 360 365 Ile Thr Thr His Ser Phe Asn Cys Gly Gly Glu Phe Phe Tyr Cys Asn 370 375 380 Thr Ser Gly Leu Phe Asn Ser Ile Trp Asn Gly Ser Met Ser Asn Asp 385 390 395 400 Met Gly Pro Asn Gly Thr Ile Thr Leu Gln Cys Arg Ile Lys Gln Ile 405 410 415 Ile Asn Met Trp Gln Arg Val Gly Gln Ala Met Tyr Ala Pro Pro Ile 420 425 430 Gln Gly Val Ile Arg Cys Glu Ser Asn Ile Thr Gly Leu Leu Leu Thr 435 440 445 Arg Asp Gly Gly Thr Asn Asn Thr Lys Asn Glu Thr Phe Arg Pro Gly 450 455 460 Gly Gly Asp Met Arg Asp Asn Trp Lys Ser Glu Leu Tyr Lys Tyr Lys 465 470 475 480 Val Val Lys Ile Glu Pro Leu Gly Val Ala Pro Thr Arg Ala Lys Arg 485 490 495 Arg Val Val Glu Arg Glu Lys Arg Ala Val Gly Leu Gly Ala Ile Phe 500 505 510 Leu Gly Phe Leu Gly Ala Ala Gly Ser Thr Met Gly Ala Ala Ser Ile 515 520 525 Thr Leu Thr Val Gln Ala Arg Gln Leu Leu Ser Gly Ile Val Gln Gln 530 535 540 Gln Ser Asn Leu Leu Arg Ala Ile Glu Ala Gln Gln His Leu Leu Lys 545 550 555 560 Leu Thr Val Trp Gly Ile Lys Gln Leu Gln Ala Arg Val Leu Ala Val 565 570 575 Glu Arg Tyr Leu Gln Asp Gln Gln Leu Leu Gly Ile Trp Gly Cys Ser 580 585 590 Gly Lys Leu Ile Cys Thr Thr Thr Val Pro Trp Asn Ser Ser Trp Ser 595 600 605 Asn Lys Ser Gln Glu Asp Ile Trp Asn Asn Met Thr Trp Leu Gln Trp 610 615 620 Glu Lys Glu Ile Ser Ser Tyr Thr Gly Ile Ile Tyr Gln Leu Ile Glu 625 630 635 640 Glu Ser Gln Asn Gln Gln Glu Lys Asn Glu Leu Asp Leu Leu Ala Leu 645 650 655 Asp Lys Trp Ala Asn Leu Asn Trp Phe Asn Ile Ser Asn Trp Leu Trp 660 665 670 Tyr Ile Arg Leu Phe Val Ile Ile Val Gly Gly Leu Ile Gly Leu Arg 675 680 685 Ile Val Phe Thr Val Leu Ser Ile Ile Asn Arg Val Arg Gln Gly Tyr 690 695 700 Ser Pro Leu Ser Phe Gln Thr Leu Ala Pro Ile Pro Glu Gly Leu Gly 705 710 715 720 Arg Pro Gly Arg Ile Glu Glu Glu Gly Gly Glu Gln Gly Lys Asp Arg 725 730 735 Ser Ile Arg Leu Val Ser Gly Phe Leu Ala Ile Ala Trp Asp Asp Leu 740 745 750 Arg Asn Leu Cys Leu Phe Ser Tyr His Arg Leu Arg Asp Phe Ala Leu 755 760 765 Ile Val Ala Arg Ala Val Glu Leu Leu Gly Arg Ser Ser Leu Lys Gly 770 775 780 Leu Arg Leu Gly Trp Glu Gly Leu Lys Tyr Leu Trp Asn Leu Leu Leu 785 790 795 800 Tyr Trp Gly Arg Glu Leu Lys Ile Ser Ala Ile Thr Leu Leu Asp Ala 805 810 815 Val Ala Val Ala Val Ala Gly Trp Ile Asp Arg Val Ile Glu Ile Gly 820 825 830 Gln Thr Ile Gly Arg Ala Ile Leu Asn Ile Pro Arg Arg Ile Arg Gln 835 840 845 Gly Leu Glu Arg Ala Leu Leu 850 855 12 855 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of B_HXB2R lentiviral env protein 12 Met Arg Val Met Gly Ile Gln Arg Asn Tyr Pro Cys Leu Trp Arg Trp 1 5 10 15 Gly Thr Met Ile Leu Gly Leu Ile Ile Ile Cys Asn Ala Gln Gln Leu 20 25 30 Trp Val Thr Val Tyr Tyr Gly Val Pro Val Trp Lys Asp Ala Val Thr 35 40 45 Thr Leu Phe Cys Ala Ser Asp Ala Lys Ala Tyr Asp Ala Glu Val His 50 55 60 Asn Val Trp Ala Thr His Ala Cys Val Pro Thr Asp Pro Asn Pro Gln 65 70 75 80 Glu Ile Asp Leu Val Asn Val Thr Glu Glu Phe Asn Met Trp Lys Asn 85 90 95 Asn Met Val Asp Gln Met His Glu Asp Ile Ile Ser Leu Trp Asp Gln 100 105 110 Ser Leu Lys Pro Cys Val Lys Leu Thr Pro Leu Cys Val Thr Leu Asp 115 120 125 Cys His Asn Ile Thr Ile Asn Asn Thr Asn Asn Asn Thr Asn Ile Thr 130 135 140 Asp Gly Val Arg Glu Glu Met Lys Asn Cys Ser Phe Asn Met Thr Thr 145 150 155 160 Glu Leu Arg Asp Lys Lys Gln Lys Val Tyr Ser Leu Phe Tyr Arg Leu 165 170 175 Asp Ile Val Gln Ile Asn Lys Thr Asp Asn Asn Ser Tyr Arg Leu Ile 180 185 190 Asn Cys Asn Thr Ser Thr Ile Thr Gln Ala Cys Pro Lys Val Ser Phe 195 200 205 Glu Pro Ile Pro Ile His Tyr Cys Ala Pro Ala Gly Phe Ala Ile Leu 210 215 220 Lys Cys Lys Asp Pro Glu Phe Asn Gly Lys Gly Pro Cys Arg Asn Val 225 230 235 240 Ser Thr Val Gln Cys Thr His Gly Ile Lys Pro Val Val Ser Thr Gln 245 250 255 Leu Leu Leu Asn Gly Ser Leu Ala Glu Arg Glu Ile Arg Ile Arg Ser 260 265 270 Glu Asn Phe Thr Asn Asn Ala Lys Thr Ile Ile Val Gln Leu Val Asn 275 280 285 Pro Val Lys Ile Asn Cys Ser Arg Pro Tyr Asn Thr Arg Lys Asn Ile 290 295 300 Arg Arg Tyr Ser Ile Gly Ser Gly Gln Ala Phe Tyr Val Thr Gly Lys 305 310 315 320 Ile Ile Gly Asp Ile Arg Gln Ala His Cys Asn Val Ser Arg Arg Asp 325 330 335 Trp Asn Arg Thr Ile Gln Gln Val Ala Glu Gln Leu Lys Lys Lys Phe 340 345 350 Asn Asn Lys Thr Ile Ile Phe Ala Ser Ser Ser Gly Gly Asp Ile Glu 355 360 365 Ile Thr Thr His Ser Phe Asn Cys Gly Gly Glu Phe Phe Tyr Cys Asn 370 375 380 Thr Ser Gly Leu Phe Asn Ser Ile Trp Asn Gly Ser Met Ser Asn Asp 385 390 395 400 Met Gly Pro Asn Gly Thr Ile Thr Leu Gln Cys Arg Ile Lys Gln Ile 405 410 415 Ile Asn Met Trp Gln Arg Val Gly Gln Ala Met Tyr Ala Pro Pro Ile 420 425 430 Gln Gly Val Ile Arg Cys Glu Ser Asn Ile Thr Gly Leu Leu Leu Thr 435 440 445 Arg Asp Gly Gly Thr Asn Asn Thr Lys Asn Glu Thr Phe Arg Pro Gly 450 455 460 Gly Gly Asp Met Arg Asp Asn Trp Lys Ser Glu Leu Tyr Lys Tyr Lys 465 470 475 480 Val Val Lys Ile Glu Pro Leu Gly Val Ala Pro Thr Arg Ala Lys Arg 485 490 495 Arg Val Val Glu Arg Glu Lys Arg Ala Val Gly Leu Gly Ala Ile Phe 500 505 510 Leu Gly Phe Leu Gly Ala Ala Gly Ser Thr Met Gly Ala Ala Ser Ile 515 520 525 Thr Leu Thr Val Gln Ala Arg Gln Leu Leu Ser Gly Ile Val Gln Gln 530 535 540 Gln Ser Asn Leu Leu Arg Ala Ile Glu Ala Gln Gln His Leu Leu Lys 545 550 555 560 Leu Thr Val Trp Gly Ile Lys Gln Leu Gln Ala Arg Val Leu Ala Val 565 570 575 Glu Arg Tyr Leu Gln Asp Gln Gln Leu Leu Gly Ile Trp Gly Cys Ser 580 585 590 Gly Lys Leu Ile Cys Thr Thr Thr Val Pro Trp Asn Ser Ser Trp Ser 595 600 605 Asn Lys Ser Gln Glu Asp Ile Trp Asn Asn Met Thr Trp Leu Gln Trp 610 615 620 Glu Lys Glu Ile Ser Ser Tyr Thr Gly Ile Ile Tyr Gln Leu Ile Glu 625 630 635 640 Glu Ser Gln Asn Gln Gln Glu Lys Asn Glu Leu Asp Leu Leu Ala Leu 645 650 655 Asp Lys Trp Ala Asn Leu Asn Trp Phe Asn Ile Ser Asn Trp Leu Trp 660 665 670 Tyr Ile Arg Leu Phe Val Ile Ile Val Gly Gly Leu Ile Gly Leu Arg 675 680 685 Ile Val Phe Thr Val Leu Ser Ile Ile Asn Arg Val Arg Gln Gly Tyr 690 695 700 Ser Pro Leu Ser Phe Gln Thr Leu Ala Pro Ile Pro Glu Gly Leu Gly 705 710 715 720 Arg Pro Gly Arg Ile Glu Glu Glu Gly Gly Glu Gln Gly Lys Asp Arg 725 730 735 Ser Ile Arg Leu Val Ser Gly Phe Leu Ala Ile Ala Trp Asp Asp Leu 740 745 750 Arg Asn Leu Cys Leu Phe Ser Tyr His Arg Leu Arg Asp Phe Ala Leu 755 760 765 Ile Val Ala Arg Ala Val Glu Leu Leu Gly Arg Ser Ser Leu Lys Gly 770 775 780 Leu Arg Leu Gly Trp Glu Gly Leu Lys Tyr Leu Trp Asn Leu Leu Leu 785 790 795 800 Tyr Trp Gly Arg Glu Leu Lys Ile Ser Ala Ile Thr Leu Leu Asp Ala 805 810 815 Val Ala Val Ala Val Ala Gly Trp Ile Asp Arg Val Ile Glu Ile Gly 820 825 830 Gln Thr Ile Gly Arg Ala Ile Leu Asn Ile Pro Arg Arg Ile Arg Gln 835 840 845 Gly Leu Glu Arg Ala Leu Leu 850 855 13 853 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of D_ELI lentiviral env protein 13 Met Arg Ala Arg Gly Ile Glu Arg Asn Cys Gln Asn Trp Trp Lys Trp 1 5 10 15 Gly Ile Met Leu Leu Gly Ile Leu Met Thr Cys Ser Ala Ala Asp Asn 20 25 30 Leu Trp Val Thr Val Tyr Tyr Gly Val Pro Val Trp Lys Glu Ala Thr 35 40 45 Thr Thr Leu Phe Cys Ala Ser Asp Ala Lys Ser Tyr Glu Thr Glu Ala 50 55 60 His Asn Ile Trp Ala Thr His Ala Cys Val Pro Thr Asp Pro Asn Pro 65 70 75 80 Gln Glu Ile Ala Leu Glu Asn Val Thr Glu Asn Phe Asn Met Trp Lys 85 90 95 Asn Asn Met Val Glu Gln Met His Glu Asp Ile Ile Ser Leu Trp Asp 100 105 110 Gln Ser Leu Lys Pro Cys Val Lys Leu Thr Pro Leu Cys Val Thr Leu 115 120 125 Asn Cys Ser Asp Glu Leu Arg Asn Asn Gly Thr Met Gly Asn Asn Val 130 135 140 Thr Thr Glu Glu Lys Gly Met Lys Asn Cys Ser Phe Asn Val Thr Thr 145 150 155 160 Val Leu Lys Asp Lys Lys Gln Gln Val Tyr Ala Leu Phe Tyr Arg Leu 165 170 175 Asp Ile Val Pro Ile Asp Asn Asp Ser Ser Thr Asn Ser Thr Asn Tyr 180 185 190 Arg Leu Ile Asn Cys Asn Thr Ser Ala Ile Thr Gln Ala Cys Pro Lys 195 200 205 Val Ser Phe Glu Pro Ile Pro Ile His Tyr Cys Ala Pro Ala Gly Phe 210 215 220 Ala Ile Leu Lys Cys Arg Asp Lys Lys Phe Asn Gly Thr Gly Pro Cys 225 230 235 240 Thr Asn Val Ser Thr Val Gln Cys Thr His Gly Ile Arg Pro Val Val 245 250 255 Ser Thr Gln Leu Leu Leu Asn Gly Ser Leu Ala Glu Glu Glu Val Ile 260 265 270 Ile Arg Ser Glu Asn Leu Thr Asn Asn Ala Lys Asn Ile Ile Ala His 275 280 285 Leu Asn Glu Ser Val Lys Ile Thr Cys Ala Arg Pro Tyr Gln Asn Thr 290 295 300 Arg Gln Arg Thr Pro Ile Gly Leu Gly Gln Ser Leu Tyr Thr Thr Arg 305 310 315 320 Ser Arg Ser Ile Ile Gly Gln Ala His Cys Asn Ile Ser Arg Ala Gln 325 330 335 Trp Ser Lys Thr Leu Gln Gln Val Ala Arg Lys Leu Gly Thr Leu Leu 340 345 350 Asn Lys Thr Ile Ile Lys Phe Lys Pro Ser Ser Gly Gly Asp Pro Glu 355 360 365 Ile Thr Thr His Ser Phe Asn Cys Gly Gly Glu Phe Phe Tyr Cys Asn 370 375 380 Thr Ser Gly Leu Phe Asn Ser Thr Trp Asn Ile Ser Ala Trp Asn Asn 385 390 395 400 Ile Thr Glu Ser Asn Asn Ser Thr Asn Thr Asn Ile Thr Leu Gln Cys 405 410 415 Arg Ile Lys Gln Ile Ile Lys Met Val Ala Gly Arg Lys Ala Ile Tyr 420 425 430 Ala Pro Pro Ile Glu Arg Asn Ile Leu Cys Ser Ser Asn Ile Thr Gly 435 440 445 Leu Leu Leu Thr Arg Asp Gly Gly Ile Asn Asn Ser Thr Asn Glu Thr 450 455 460 Phe Arg Pro Gly Gly Gly Asp Met Arg Asp Asn Trp Arg Ser Glu Leu 465 470 475 480 Tyr Lys Tyr Lys Val Val Gln Ile Glu Pro Leu Gly Val Ala Pro Thr 485 490 495 Arg Ala Lys Arg Arg Val Val Glu Arg Glu Lys Arg Ala Ile Gly Leu 500 505 510 Gly Ala Met Phe Leu Gly Phe Leu Gly Ala Ala Gly Ser Thr Met Gly 515 520 525 Ala Arg Ser Val Thr Leu Thr Val Gln Ala Arg Gln Leu Met Ser Gly 530 535 540 Ile Val Gln Gln Gln Asn Asn Leu Leu Arg Ala Ile Glu Ala Gln Gln 545 550 555 560 His Leu Leu Gln Leu Thr Val Trp Gly Ile Lys Gln Leu Gln Ala Arg 565 570 575 Ile Leu Ala Val Glu Arg Tyr Leu Lys Asp Gln Gln Leu Leu Gly Ile 580 585 590 Trp Gly Cys Ser Gly Lys His Ile Cys Thr Thr Asn Val Pro Trp Asn 595 600 605 Ser Ser Trp Ser Asn Arg Ser Leu Asn Glu Ile Trp Gln Asn Met Thr 610 615 620 Trp Met Glu Trp Glu Arg Glu Ile Asp Asn Tyr Thr Gly Leu Ile Tyr 625 630 635 640 Ser Leu Ile Glu Glu Ser Gln Thr Gln Gln Glu Lys Asn Glu Lys Glu 645 650 655 Leu Leu Glu Leu Asp Lys Trp Ala Ser Leu Trp Asn Trp Phe Ser Ile 660 665 670 Thr Gln Trp Leu Trp Tyr Ile Lys Ile Phe Ile Met Ile Ile Gly Gly 675 680 685 Leu Ile Gly Leu Arg Ile Val Phe Ala Val Leu Ser Leu Val Asn Arg 690 695 700 Val Arg Gln Gly Tyr Ser Pro Leu Ser Phe Gln Thr Leu Leu Pro Ala 705 710 715 720 Pro Arg Gly Pro Asp Arg Pro Glu Gly Thr Glu Glu Glu Gly Gly Glu 725 730 735 Arg Gly Arg Asp Arg Ser Val Arg Leu Leu Asn Gly Phe Ser Ala Leu 740 745 750 Ile Trp Asp Asp Leu Arg Ser Leu Cys Leu Phe Ser Tyr His Arg Leu 755 760 765 Arg Asp Leu Ile Leu Ile Ala Val Arg Ile Val Glu Leu Leu Gly Arg 770 775 780 Arg Gly Trp Asp Ile Leu Lys Tyr Leu Trp Asn Leu Leu Gln Tyr Trp 785 790 795 800 Ser Gln Glu Leu Arg Asn Ser Ala Ser Ser Leu Phe Asp Ala Ile Ala 805 810 815 Ile Ala Val Ala Glu Gly Thr Asp Arg Val Ile Glu Ile Ile Gln Arg 820 825 830 Ala Cys Arg Ala Val Leu Asn Ile Pro Arg Arg Ile Arg Gln Gly Leu 835 840 845 Glu Arg Ser Leu Leu 850 14 875 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of C-MVP5180 lentiviral env protein 14 Met Thr Val Thr Met Lys Val Met Lys Lys Asn Asn Arg Lys Ser Trp 1 5 10 15 Ser Leu Tyr Ile Ala Met Ala Leu Leu Ile Pro Cys Leu Ser Tyr Ser 20 25 30 Lys Gln Leu Tyr Ala Thr Val Tyr Ser Gly Val Pro Val Trp Glu Glu 35 40 45 Ala Ala Pro Val Leu Phe Cys Ala Ser Asp Ala Asn Leu Thr Ser Thr 50 55 60 Glu Gln His Asn Ile Trp Ala Ser Gln Ala Cys Val Pro Thr Asp Pro 65 70 75 80 Asn Pro His Glu Phe Pro Leu Gly Asn Val Thr Asp Asn Phe Asp Ile 85 90 95 Trp Lys Asn Tyr Met Val Asp Gln Met His Glu Asp Ile Ile Ser Leu 100 105 110 Trp Glu Gln Ser Leu Lys Pro Cys Glu Lys Met Thr Phe Leu Cys Val 115 120 125 Gln Met Asn Cys Val Asp Leu Gln Thr Asn Lys Thr Gly Leu Leu Asn 130 135 140 Glu Thr Ile Asn Glu Met Arg Asn Cys Ser Phe Asn Val Thr Thr Val 145 150 155 160 Leu Thr Asp Lys Lys Glu Gln Lys Gln Ala Leu Phe Tyr Val Ser Asp 165 170 175 Leu Ser Lys Val Asn Asp Ser Asn Ala Val Asn Gly Thr Thr Tyr Met 180 185 190 Leu Thr Asn Cys Asn Ser Thr Ile Ile Lys Gln Ala Cys Pro Lys Val 195 200 205 Ser Phe Glu Pro Ile Pro Ile His Tyr Cys Ala Pro Thr Gly Tyr Ala 210 215 220 Ile Phe Lys Cys Asn Asp Thr Asp Phe Asn Gly Thr Gly Leu Cys His 225 230 235 240 Asn Ile Ser Val Val Thr Cys Thr His Gly Ile Lys Pro Thr Val Ser 245 250 255 Thr Gln Leu Ile Leu Asn Gly Thr Leu Ser Arg Glu Lys Ile Arg Ile 260 265 270 Met Gly Lys Asn Ile Thr Glu Ser Ala Lys Asn Ile Ile Val Thr Leu 275 280 285 Asn Thr Pro Ile Asn Met Thr Cys Ile Arg Glu Gly Ile Ala Glu Val 290 295 300 Gln Asp Ile Tyr Thr Gly Pro Met Arg Trp Arg Ser Met Thr Leu Lys 305 310 315 320 Arg Ser Asn Asn Thr Ser Pro Arg Ser Arg Val Ala Tyr Cys Thr Tyr 325 330 335 Asn Lys Thr Val Trp Glu Asn Ala Leu Gln Gln Thr Ala Ile Arg Tyr 340 345 350 Leu Asn Leu Val Asn Gln Thr Glu Asn Val Thr Ile Ile Phe Ser Arg 355 360 365 Thr Ser Gly Gly Asp Ala Glu Val Ser His Leu His Phe Asn Cys His 370 375 380 Gly Glu Phe Phe Tyr Cys Asn Thr Ser Gly Met Phe Asn Tyr Thr Phe 385 390 395 400 Ile Asn Cys Thr Lys Ser Gly Cys Gln Glu Ile Lys Gly Ser Asn Glu 405 410 415 Thr Asn Lys Asn Gly Thr Ile Pro Cys Lys Leu Arg Gln Leu Val Arg 420 425 430 Ser Trp Met Lys Gly Glu Ser Arg Ile Tyr Ala Pro Pro Ile Pro Gly 435 440 445 Asn Leu Thr Cys His Ser Asn Ile Thr Gly Met Ile Leu Gln Leu Asp 450 455 460 Gln Pro Trp Asn Ser Thr Gly Glu Asn Thr Leu Arg Pro Val Gly Gly 465 470 475 480 Asp Met Lys Asp Ile Trp Arg Thr Lys Leu Tyr Asn Tyr Lys Val Val 485 490 495 Gln Ile Lys Pro Phe Ser Val Ala Pro Thr Lys Met Ser Arg Pro Ile 500 505 510 Ile Asn Ile His Thr Pro His Arg Glu Lys Arg Ala Val Gly Leu Gly 515 520 525 Met Leu Phe Leu Gly Val Leu Ser Ala Ala Gly Ser Thr Met Gly Ala 530 535 540 Ala Ala Thr Ala Leu Thr Val Arg Thr His Ser Val Leu Lys Gly Ile 545 550 555 560 Val Gln Gln Gln Asp Asn Leu Leu Arg Ala Ile Gln Ala Gln Gln His 565 570 575 Leu Leu Arg Leu Ser Val Trp Gly Ile Arg Gln Leu Arg Ala Arg Leu 580 585 590 Gln Ala Leu Glu Thr Leu Ile Asn Gln Gln Arg Leu Asn Leu Trp Gly 595 600 605 Cys Lys Gly Lys Leu Ile Cys Tyr Thr Ser Val Lys Trp Asn Thr Ser 610 615 620 Trp Ser Gly Arg Tyr Asn Asp Asp Ser Ile Trp Asp Asn Leu Thr Trp 625 630 635 640 Gln Gln Trp Asp Gln His Ile Asn Asn Val Ser Ser Ile Ile Tyr Asp 645 650 655 Glu Ile Gln Ala Ala Gln Asp Gln Gln Glu Lys Asn Val Lys Ala Leu 660 665 670 Leu Glu Leu Asp Glu Trp Ala Ser Leu Trp Asn Trp Phe Asp Ile Thr 675 680 685 Lys Trp Leu Trp Tyr Ile Lys Ile Ala Ile Ile Ile Val Gly Ala Leu 690 695 700 Ile Gly Ile Arg Val Ile Met Ile Ile Leu Asn Leu Val Lys Asn Ile 705 710 715 720 Arg Gln Gly Tyr Gln Pro Leu Ser Leu Gln Ile Pro Val Pro His Arg 725 730 735 Gln Glu Ala Glu Thr Pro Gly Arg Thr Gly Glu Glu Gly Gly Glu Gly 740 745 750 Asp Arg Pro Lys Trp Thr Ala Leu Pro Pro Gly Phe Leu Gln Gln Leu 755 760 765 Tyr Thr Asp Leu Arg Thr Ile Ile Leu Trp Thr Tyr His Leu Leu Ser 770 775 780 Asn Leu Ile Ser Gly Ile Arg Arg Leu Ile Asp Tyr Leu Gly Leu Gly 785 790 795 800 Leu Trp Ile Leu Gly Gln Lys Thr Ile Glu Ala Cys Arg Leu Cys Gly 805 810 815 Ala Val Met Gln Tyr Trp Leu Gln Glu Leu Lys Asn Ser Ala Thr Asn 820 825 830 Leu Leu Asp Thr Ile Ala Val Ser Val Ala Asn Trp Thr Asp Gly Ile 835 840 845 Ile Leu Gly Leu Gln Arg Ile Gly Gln Gly Phe Leu His Ile Pro Arg 850 855 860 Arg Ile Arg Gln Gly Ala Glu Arg Ile Leu Val 865 870 875 15 862 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of O_ANT70 lentiviral env protein 15 Met Ile Val Thr Met Lys Ala Met Glu Lys Arg Asn Lys Lys Leu Trp 1 5 10 15 Thr Leu Tyr Leu Ala Met Ala Leu Ile Thr Pro Cys Leu Ser Leu Arg 20 25 30 Gln Leu Tyr Ala Thr Val Tyr Ala Gly Val Pro Val Trp Glu Asp Ala 35 40 45 Thr Pro Val Leu Phe Cys Ala Ser Asp Ala Asn Leu Thr Ser Thr Glu 50 55 60 Lys His Asn Ile Trp Ala Ser Gln Ala Cys Val Pro Thr Asp Pro Thr 65 70 75 80 Pro Tyr Glu Tyr Pro Leu His Asn Val Thr Asp Asp Phe Asn Ile Trp 85 90 95 Lys Asn Tyr Met Val Glu Gln Met Gln Glu Asp Ile Ile Ser Leu Trp 100 105 110 Asp Gln Ser Leu Lys Pro Cys Val Gln Met Thr Phe Leu Cys Val Gln 115 120 125 Met Glu Cys Thr Asn Ile Ala Gly Thr Thr Asn Glu Asn Leu Met Lys 130 135 140 Lys Cys Glu Phe Asn Val Thr Thr Val Ile Lys Asp Lys Lys Glu Lys 145 150 155 160 Lys Gln Ala Leu Phe Tyr Val Ser Asp Leu Met Glu Leu Asn Glu Thr 165 170 175 Ser Ser Thr Asn Lys Thr Asn Ser Lys Met Tyr Thr Leu Thr Asn Cys 180 185 190 Asn Ser Thr Thr Ile Thr Gln Ala Cys Pro Lys Val Ser Phe Glu Pro 195 200 205 Ile Pro Ile His Tyr Cys Ala Pro Ala Gly Tyr Ala Ile Phe Lys Cys 210 215 220 Asn Ser Thr Glu Phe Asn Gly Thr Gly Thr Cys Arg Asn Ile Thr Val 225 230 235 240 Val Thr Cys Thr His Gly Ile Arg Pro Thr Val Ser Thr Gln Leu Ile 245 250 255 Leu Asn Gly Thr Leu Ser Lys Gly Lys Ile Arg Met Met Ala Lys Asp 260 265 270 Ile Leu Glu Gly Gly Lys Asn Ile Ile Val Thr Leu Asn Ser Thr Leu 275 280 285 Asn Met Thr Cys Glu Arg Pro Gln Ile Asp Ile Gln Glu Met Arg Ile 290 295 300 Gly Pro Met Ala Trp Tyr Ser Met Gly Ile Gly Gly Thr Ala Gly Asn 305 310 315 320 Ser Ser Arg Ala Ala Tyr Cys Lys Tyr Asn Ala Thr Asp Trp Gly Lys 325 330 335 Ile Leu Lys Gln Thr Ala Glu Arg Tyr Leu Glu Leu Val Asn Asn Thr 340 345 350 Gly Ser Ile Asn Met Thr Phe Asn His Ser Ser Gly Gly Asp Leu Glu 355 360 365 Val Thr His Leu His Phe Asn Cys His Gly Glu Phe Phe Tyr Cys Asn 370 375 380 Thr Ala Lys Met Phe Asn Tyr Thr Phe Ser Cys Asn Gly Thr Thr Cys 385 390 395 400 Ser Val Ser Asn Val Ser Gln Gly Asn Asn Gly Thr Leu Pro Cys Lys 405 410 415 Leu Arg Gln Val Val Arg Ser Trp Ile Arg Gly Gln Ser Gly Leu Tyr 420 425 430 Ala Pro Pro Ile Lys Gly Asn Leu Thr Cys Met Ser Asn Ile Thr Gly 435 440 445 Met Ile Leu Gln Met Asp Asn Thr Trp Asn Ser Ser Asn Asn Asn Val 450 455 460 Thr Phe Arg Pro Ile Gly Gly Asp Met Lys Asp Ile Trp Arg Thr Glu 465 470 475 480 Leu Phe Asn Tyr Lys Val Val Arg Val Lys Pro Phe Ser Val Ala Pro 485 490 495 Thr Arg Ile Ala Arg Pro Val Ile Ser Thr Arg Thr His Arg Glu Lys 500 505 510 Arg Ala Val Gly Leu Gly Met Leu Phe Leu Gly Val Leu Ser Ala Ala 515 520 525 Gly Ser Thr Met Gly Ala Ala Ala Thr Thr Leu Ala Val Gln Thr His 530 535 540 Thr Leu Leu Lys Gly Ile Val Gln Gln Gln Asp Asn Leu Leu Arg Ala 545 550 555 560 Ile Gln Ala Gln Gln Gln Leu Leu Arg Leu Ser Trp Gly Ile Arg Gln 565 570 575 Leu Arg Ala Arg Leu Leu Ala Leu Glu Thr Leu Leu Gln Asn Gln Gln 580 585 590 Leu Leu Ser Leu Trp Gly Cys Lys Gly Lys Leu Val Cys Tyr Thr Ser 595 600 605 Val Lys Trp Asn Arg Thr Trp Ile Gly Asn Glu Ser Ile Trp Asp Thr 610 615 620 Leu Thr Trp Gln Glu Trp Asp Arg Gln Ile Ser Asn Ile Ser Ser Thr 625 630 635 640 Ile Tyr Glu Glu Ile Gln Lys Ala Gln Val Gln Gln Glu Gln Asn Glu 645 650 655 Lys Lys Leu Leu Glu Leu Asp Glu Trp Ala Ser Ile Trp Asn Trp Leu 660 665 670 Asp Ile Thr Lys Trp Leu Trp Tyr Ile Lys Ile Ala Ile Ile Ile Val 675 680 685 Gly Ala Leu Val Gly Val Arg Val Ile Met Ile Val Leu Asn Ile Val 690 695 700 Lys Asn Ile Arg Gln Gly Tyr Gln Pro Leu Ser Leu Gln Ile Pro Asn 705 710 715 720 His His Gln Glu Glu Ala Gly Thr Pro Gly Arg Thr Gly Gly Gly Gly 725 730 735 Gly Glu Glu Gly Arg Pro Arg Trp Ile Pro Ser Pro Gln Gly Phe Leu 740 745 750 Pro Leu Leu Tyr Thr Asp Leu Arg Thr Ile Ile Leu Trp Thr Tyr His 755 760 765 Leu Leu Ser Asn Leu Ala Ser Gly Ile Gln Lys Val Ile Ser Tyr Leu 770 775 780 Arg Leu Gly Leu Trp Ile Leu Gly Gln Lys Ile Ile Asn Val Cys Arg 785 790 795 800 Ile Cys Ala Ala Val Thr Gln Tyr Trp Leu Gln Glu Leu Gln Asn Ser 805 810 815 Ala Thr Ser Leu Leu Asp Thr Leu Ala Val Ala Val Ala Asn Trp Thr 820 825 830 Asp Gly Ile Ile Ala Gly Ile Gln Arg Ile Gly Thr Gly Ile Arg Asn 835 840 845 Ile Pro Arg Arg Ile Arg Gln Gly Leu Glu Arg Ser Leu Leu 850 855 860 16 854 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of SIVcpzGAB1 lentiviral env protein 16 Met Lys Val Met Glu Lys Lys Lys Arg Asp Trp Asn Ser Leu Ser Ile 1 5 10 15 Ile Thr Ile Ile Thr Ile Ile Leu Leu Thr Pro Cys Leu Thr Ser Glu 20 25 30 Leu Trp Val Thr Val Tyr Tyr Gly Val Pro Val Trp His Asp Ala Asp 35 40 45 Pro Val Leu Phe Cys Ala Ser Asp Ala Lys Ala His Ser Thr Glu Ala 50 55 60 His Asn Ile Trp Ala Thr Gln Ala Cys Val Pro Thr Asp Pro Ser Pro 65 70 75 80 Gln Glu Val Phe Leu Pro Asn Val Ile Glu Ser Phe Asn Met Trp Lys 85 90 95 Asn Asn Met Val Asp Gln Met His Glu Asp Ile Ile Ser Leu Trp Asp 100 105 110 Gln Ser Leu Lys Pro Cys Val Lys Leu Thr Pro Leu Cys Val Thr Leu 115 120 125 Gln Cys Ser Lys Ala Asn Phe Ser Gln Ala Lys Asn Leu Thr Asn Gln 130 135 140 Thr Ser Ser Pro Pro Leu Glu Met Lys Asn Cys Ser Phe Asn Val Thr 145 150 155 160 Thr Glu Leu Arg Asp Lys Lys Lys Gln Val Tyr Ser Leu Phe Tyr Val 165 170 175 Glu Asp Val Val Asn Leu Gly Asn Glu Asn Asn Thr Tyr Arg Ile Ile 180 185 190 Asn Cys Asn Thr Thr Ala Ile Thr Gln Ala Cys Pro Lys Thr Ser Phe 195 200 205 Glu Pro Ile Pro Ile His Tyr Cys Ala Pro Ala Gly Phe Ala Ile Leu 210 215 220 Lys Cys Asn Asp Lys Asp Phe Ser Gly Lys Gly Lys Cys Thr Asn Val 225 230 235 240 Ser Thr Val His Cys Thr His Gly Ile Lys Pro Val Val Thr Thr Gln 245 250 255 Leu Leu Ile Asn Gly Ser Leu Ala Glu Gly Asn Ile Thr Val Arg Val 260 265 270 Glu Asn Lys Ser Lys Asn Thr Asp Val Trp Ile Val Gln Leu Val Glu 275 280 285 Ala Val Ser Leu Asn Cys His Arg Pro Gly Asn Asn Thr Arg Gly Glu 290 295 300 Val Gln Ile Gly Pro Gly Met Thr Phe Tyr Asn Ile Glu Asn Val Val 305 310 315 320 Gly Asp Thr Arg Ser Ala Tyr Cys Lys Ile Asn Gly Thr Thr Trp Asn 325 330 335 Arg Thr Val Glu Glu Val Lys Lys Ala Leu Ala Thr Ser Ser Asn Arg 340 345 350 Thr Ala Ala Asn Ile Thr Leu Asn Arg Ala Ser Gly Gly Asp Pro Glu 355 360 365 Val Thr His His Met Phe Asn Cys Gly Gly Glu Phe Phe Tyr Cys Asn 370 375 380 Thr Ser Gln Ile Phe Thr Asp Asn Ile Thr Asn Gly Ile Ile Ile Leu 385 390 395 400 Pro Cys Arg Ile Arg Gln Ile Val Ser Ser Trp Met Arg Val Gly Arg 405 410 415 Gly Ile Tyr Ala Pro Pro Ile Arg Gly Asn Ile Thr Cys Asn Ser Asn 420 425 430 Ile Thr Gly Leu Leu Leu Thr Ser Asp Thr Pro Val Thr Asn Asn Ser 435 440 445 Gly Asn Leu Thr Phe Arg Pro Thr Gly Gly Asn Met Lys Asp Ile Trp 450 455 460 Arg Ser Glu Leu Tyr Lys Tyr Lys Val Val Arg Ile Glu Pro Leu Ser 465 470 475 480 Val Ala Pro Thr Lys Ala Arg Arg His Thr Val Ala Arg Gln Lys Asp 485 490 495 Arg Gln Lys Arg Ala Ala Phe Gly Leu Gly Ala Leu Phe Leu Gly Phe 500 505 510 Leu Gly Ala Ala Gly Ser Thr Met Gly Ala Ala Ala Val Thr Leu Thr 515 520 525 Val Gln Ala Arg Gln Leu Leu Ser Gly Ile Val Gln Gln Gln Asn Asn 530 535 540 Leu Leu Lys Ala Ile Glu Ala Gln Gln His Leu Leu Gln Leu Ser Ile 545 550 555 560 Trp Gly Val Lys Gln Leu Gln Ala Arg Leu Leu Ala Val Glu Arg Tyr 565 570 575 Leu Gln Asp Gln Gln Ile Leu Gly Leu Trp Gly Cys Ser Gly Lys Ala 580 585 590 Val Cys Tyr Thr Thr Val Pro Trp Asn Asn Ser Trp Pro Gly Ser Asn 595 600 605 Ser Thr Asp Asp Ile Trp Gly Asn Leu Thr Trp Gln Gln Trp Asp Lys 610 615 620 Leu Val Ser Asn Tyr Thr Gly Lys Ile Phe Gly Leu Leu Glu Glu Ala 625 630 635 640 Gln Ser Gln Gln Glu Lys Asn Glu Arg Asp Leu Leu Glu Leu Asp Gln 645 650 655 Trp Ala Ser Leu Trp Asn Trp Phe Asp Ile Thr Lys Trp Leu Trp Tyr 660 665 670 Ile Lys Ile Phe Leu Met Ala Val Gly Gly Ile Ile Gly Leu Arg Ile 675 680 685 Ile Met Thr Val Phe Ser Val Val Arg Arg Val Arg Gln Gly Tyr Ser 690 695 700 Pro Leu Ser Leu Gln Thr Leu Ile Pro Val Gln Arg Glu Gln Gly Arg 705 710 715 720 Leu Gly Glu Ile Asp Glu Gly Gly Gly Glu Gln Asp Arg Ser Arg Ser 725 730 735 Val Arg Leu Val Glu Gly Cys Leu Pro Leu Ile Trp Asp Asp Leu Arg 740 745 750 Asn Leu Gly Ile Trp Ser Tyr Gln Ser Leu Thr Ser Leu Ala Cys Asn 755 760 765 Val Trp Arg Gln Leu Lys Thr Leu Gly His Leu Ile Leu His Ser Leu 770 775 780 Arg Leu Leu Arg Glu Arg Leu Cys Leu Leu Gly Gly Ile Ile Gln Tyr 785 790 795 800 Trp Gly Lys Glu Leu Lys Ile Ser Ala Ile Ser Leu Leu Asp Ala Thr 805 810 815 Ala Ile Ala Val Ala Glu Gly Thr Asp Arg Ile Ile Glu Ala Phe Gln 820 825 830 Val Thr Leu Arg Ile Ile Arg Asn Ile Pro Arg Arg Ile Arg Gln Gly 835 840 845 Leu Glu Arg Ala Leu Leu 850 17 854 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of SIVcpzANT lentiviral env protein 17 Met Arg Lys Pro Ile His Ile Ile Trp Gly Leu Ala Leu Leu Ile Gln 1 5 10 15 Phe Ile Glu Lys Gly Thr Asn Glu Asp Tyr Val Thr Val Phe Tyr Gly 20 25 30 Val Pro Val Trp Arg Asn Ala Thr Pro Thr Leu Phe Cys Ala Thr Asn 35 40 45 Ala Ser Met Thr Ser Thr Glu Val His Asn Val Trp Ala Thr Thr Ser 50 55 60 Cys Val Pro Ile Asp Pro Asp Pro Ile Val Val Arg Leu Asn Thr Ser 65 70 75 80 Val Trp Phe Asn Ala Tyr Lys Asn Tyr Met Val Glu Ser Met Thr Glu 85 90 95 Asp Met Gln Leu Phe Gln Gln Ser His Lys Pro Cys Val Lys Leu Thr 100 105 110 Pro Met Cys Ile Lys Met Asn Cys Thr Gly Tyr Asn Gly Thr Pro Thr 115 120 125 Thr Pro Ser Thr Thr Thr Ser Thr Val Thr Pro Lys Thr Thr Thr Pro 130 135 140 Ile Val Asp Gly Met Lys Leu Gln Glu Cys Asn Phe Asn Gln Ser Thr 145 150 155 160 Gly Phe Lys Asp Lys Lys Gln Lys Met Lys Ala Ile Phe Tyr Lys Gly 165 170 175 Asp Leu Met Lys Cys Gln Asp Asn Asn Glu Thr Asn Cys Tyr Tyr Leu 180 185 190 Trp His Cys Asn Thr Thr Thr Ile Thr Gln Ser Cys Glu Lys Ser Thr 195 200 205 Phe Glu Pro Ile Pro Ile His Tyr Cys Ala Pro Ala Gly Tyr Ala Ile 210 215 220 Leu Arg Cys Glu Asp Glu Asp Phe Thr Gly Val Gly Met Cys Lys Asn 225 230 235 240 Val Ser Val Val His Cys Thr His Gly Ile Ser Pro Met Val Ala Thr 245 250 255 Trp Leu Leu Leu Asn Gly Thr Tyr Gln Thr Asn Thr Ser Val Val Met 260 265 270 Asn Gly Arg Lys Asn Glu Ser Val Leu Val Arg Phe Gly Lys Glu Phe 275 280 285 Glu Asn Leu Thr Ile Thr Cys Ile Arg Pro Gly Asn Arg Thr Val Arg 290 295 300 Asn Leu Gln Ile Gly Pro Gly Met Thr Phe Tyr Asn Val Glu Ile Ala 305 310 315 320 Thr Gly Asp Thr Arg Lys Ala Phe Cys Thr Val Asn Lys Thr Leu Trp 325 330 335 Glu Gln Ala Arg Asn Lys Thr Glu His Val Leu Ala Glu His Trp Lys 340 345 350 Lys Val Asp Asn Lys Thr Asn Ala Lys Thr Ile Trp Thr Phe Gln Asp 355 360 365 Gly Asp Pro Glu Val Lys Val His Trp Phe Asn Cys Gln Gly Glu Phe 370 375 380 Phe Tyr Cys Asp Ile Thr Pro Trp Phe Asn Ala Thr Tyr Thr Gly Asn 385 390 395 400 Leu Ile Thr Asn Gly Ala Leu Ile Ala His Cys Arg Ile Lys Gln Ile 405 410 415 Val Asn His Trp Gly Ile Val Ser Lys Gly Ile Tyr Leu Ala Pro Arg 420 425 430 Arg Gly Asn Val Ser Cys Thr Ser Ser Ile Thr Gly Ile Met Leu Glu 435 440 445 Gly Gln Ile Tyr Asn Glu Thr Val Lys Val Ser Pro Ala Ala Arg Val 450 455 460 Ala Asp Gln Trp Arg Ala Glu Leu Ser Arg Tyr Gln Val Val Glu Ile 465 470 475 480 Pro Leu Ser Val Ala Pro Thr Thr Lys Arg Pro Glu Ile Lys Gln His 485 490 495 Ser Arg Gln Lys Arg Gly Ile Gly Ile Gly Leu Phe Phe Leu Gly Leu 500 505 510 Leu Ser Ala Ala Gly Ser Thr Met Gly Ala Ala Ser Ile Ala Leu Thr 515 520 525 Ala Gln Thr Arg Asn Leu His Gly Ile Val Gln Gln Gln Ala Asn Leu 530 535 540 Leu Gln Ala Ile Glu Thr Gln Gln His Leu Leu Gln Leu Ser Val Trp 545 550 555 560 Gly Val Lys Gln Leu Gln Ala Arg Met Leu Ala Val Glu Lys Tyr Leu 565 570 575 Arg Asp Gln Gln Leu Leu Ser Leu Trp Gly Cys Ala Asp Lys Val Thr 580 585 590 Cys His Thr Thr Val Pro Trp Asn Asn Ser Trp Val Asn Phe Thr Gln 595 600 605 Thr Cys Ala Lys Asn Ser Ser Asp Ile Gln Cys Ile Trp Glu Asn Met 610 615 620 Thr Trp Gln Glu Trp Asp Arg Leu Val Gln Asn Ser Thr Gly Gln Ile 625 630 635 640 Tyr Asn Ile Leu Gln Ile Ala His Glu Gln Gln Glu Arg Asn Lys Lys 645 650 655 Glu Leu Tyr Glu Leu Asp Lys Trp Ser Ser Leu Trp Asn Trp Phe Asp 660 665 670 Ile Thr Gln Trp Leu Trp Tyr Ile Lys Ile Phe Ile Met Ile Val Gly 675 680 685 Ala Ile Val Gly Leu Arg Ile Leu Leu Val Leu Val Ser Cys Leu Arg 690 695 700 Lys Val Arg Gln Gly Tyr His Pro Leu Ser Phe Gln Ile Pro Thr Gln 705 710 715 720 Asn Gln Gln Asp Pro Glu Gln Pro Glu Glu Ile Arg Glu Glu Gly Gly 725 730 735 Arg Lys Asp Arg Ile Arg Trp Arg Ala Leu Gln His Gly Phe Phe Ala 740 745 750 Leu Leu Trp Val Asp Leu Thr Ser Ile Ile Gln Trp Ile Tyr Gln Ile 755 760 765 Cys Arg Thr Cys Leu Leu Asn Leu Trp Ala Val Leu Gln His Leu Cys 770 775 780 Arg Ile Thr Phe Arg Leu Cys Asn His Leu Glu Asn Asn Leu Ser Thr 785 790 795 800 Leu Trp Thr Ile Ile Arg Thr Glu Ile Ile Lys Asn Ile Asp Arg Leu 805 810 815 Ala Ile Trp Val Gly Glu Lys Thr Asp Ser Ile Leu Leu Ala Leu Gln 820 825 830 Thr Ile Val Arg Ile Ile Arg Glu Val Pro Arg Arg Ile Arg Gln Gly 835 840 845 Leu Glu Ile Ala Leu Asn 850 18 858 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of A_ROD lentiviral env protein 18 Met Met Asn Gln Leu Leu Ile Ala Ile Leu Leu Ala Ser Ala Cys Leu 1 5 10 15 Val Tyr Cys Thr Gln Tyr Val Thr Val Phe Tyr Gly Val Pro Thr Trp 20 25 30 Lys Asn Ala Thr Ile Pro Leu Phe Cys Ala Thr Arg Asn Arg Asp Thr 35 40 45 Trp Gly Thr Ile Gln Cys Leu Pro Asp Asn Asp Asp Tyr Gln Glu Ile 50 55 60 Thr Leu Asn Val Thr Glu Ala Phe Asp Ala Trp Asn Asn Thr Val Thr 65 70 75 80 Glu Gln Ala Ile Glu Asp Val Trp His Leu Phe Glu Thr Ser Ile Lys 85 90 95 Pro Cys Val Lys Leu Thr Pro Leu Cys Val Ala Met Lys Cys Ser Ser 100 105 110 Thr Glu Ser Ser Thr Gly Asn Asn Thr Thr Ser Lys Ser Thr Ser Thr 115 120 125 Thr Thr Thr Thr Pro Thr Asp Gln Glu Gln Glu Ile Ser Glu Asp Thr 130 135 140 Pro Cys Ala Arg Ala Asp Asn Cys Ser Gly Leu Gly Glu Glu Glu Thr 145 150 155 160 Ile Asn Cys Gln Phe Asn Met Thr Gly Leu Glu Arg Asp Lys Lys Lys 165 170 175 Gln Tyr Asn Glu Thr Trp Tyr Ser Lys Asp Val Val Cys Glu Thr Asn 180 185 190 Asn Ser Thr Asn Gln Thr Gln Cys Tyr Met Asn His Cys Asn Thr Ser 195 200 205 Val Ile Thr Glu Ser Cys Asp Lys His Tyr Trp Asp Ala Ile Arg Phe 210 215 220 Arg Tyr Cys Ala Pro Pro Gly Tyr Ala Leu Leu Arg Cys Asn Asp Thr 225 230 235 240 Asn Tyr Ser Gly Phe Ala Pro Asn Cys Ser Lys Val Val Ala Ser Thr 245 250 255 Cys Thr Arg Met Met Glu Thr Gln Thr Ser Thr Trp Phe Gly Phe Asn 260 265 270 Gly Thr Arg Ala Glu Asn Arg Thr Tyr Ile Tyr Trp His Gly Arg Asp 275 280 285 Asn Arg Thr Ile Ile Ser Leu Asn Lys Tyr Tyr Asn Leu Ser Leu His 290 295 300 Cys Lys Arg Pro Gly Asn Lys Ile Val Lys Gln Ile Met Leu Met Ser 305 310 315 320 Gly His Val Phe His Ser His Tyr Gln Pro Ile Asn Lys Arg Pro Arg 325 330 335 Gln Ala Trp Cys Trp Phe Lys Gly Lys Trp Lys Asp Ala Met Gln Glu 340 345 350 Val Lys Glu Thr Leu Ala Lys His Pro Arg Tyr Arg Gly Thr Asn Asp 355 360 365 Thr Arg Asn Ile Ser Phe Ala Ala Pro Gly Lys Gly Ser Asp Pro Glu 370 375 380 Val Ala Tyr Met Trp Thr Asn Cys Arg Gly Glu Phe Leu Tyr Cys Asn 385 390 395 400 Met Thr Trp Phe Leu Asn Trp Ile Glu Asn Lys Thr His Arg Asn Tyr 405 410 415 Ala Pro Cys His Ile Lys Gln Ile Ile Asn Thr Trp His Lys Val Gly 420 425 430 Arg Asn Val Tyr Leu Pro Pro Arg Glu Gly Glu Leu Ser Cys Asn Ser 435 440 445 Thr Val Thr Ser Ile Ile Ala Asn Ile Asp Trp Gln Asn Asn Asn Gln 450 455 460 Thr Asn Ile Thr Phe Ser Ala Glu Val Ala Glu Leu Tyr Arg Leu Glu 465 470 475 480 Leu Gly Asp Tyr Lys Leu Val Glu Ile Thr Pro Ile Gly Phe Ala Pro 485 490 495 Thr Lys Glu Lys Arg Tyr Ser Ser Ala His Gly Arg His Thr Arg Gly 500 505 510 Val Phe Val Leu Gly Phe Leu Gly Phe Leu Ala Thr Ala Gly Ser Ala 515 520 525 Met Gly Ala Ala Ser Leu Thr Val Ser Ala Gln Ser Arg Thr Leu Leu 530 535 540 Ala Gly Ile Val Gln Gln Gln Gln Gln Leu Leu Asp Val Val Lys Arg 545 550 555 560 Gln Gln Glu Leu Leu Arg Leu Thr Val Trp Gly Thr Lys Asn Leu Gln 565 570 575 Ala Arg Val Thr Ala Ile Glu Lys Tyr Leu Gln Asp Gln Ala Arg Leu 580 585 590 Asn Ser Trp Gly Cys Ala Phe Arg Gln Val Cys His Thr Thr Val Pro 595 600 605 Trp Val Asn Asp Ser Leu Ala Pro Asp Trp Asp Asn Met Thr Trp Gln 610 615 620 Glu Trp Glu Lys Gln Val Arg Tyr Leu Glu Ala Asn Ile Ser Lys Ser 625 630 635 640 Leu Glu Gln Ala Gln Ile Gln Gln Glu Lys Asn Met Tyr Glu Leu Gln 645 650 655 Lys Leu Asn Ser Trp Asp Ile Phe Gly Asn Trp Phe Asp Leu Thr Ser 660 665 670 Trp Val Lys Tyr Ile Gln Tyr Gly Val Leu Ile Ile Val Ala Val Ile 675 680 685 Ala Leu Arg Ile Val Ile Tyr Val Val Gln Met Leu Ser Arg Leu Arg 690 695 700 Lys Gly Tyr Arg Pro Val Phe Ser Ser Pro Pro Gly Tyr Ile Gln Gln 705 710 715 720 Ile His Ile His Lys Asp Arg Gly Gln Pro Ala Asn Glu Glu Thr Glu 725 730 735 Glu Asp Gly Gly Ser Asn Gly Gly Asp Arg Tyr Trp Pro Trp Pro Ile 740 745 750 Ala Tyr Ile His Phe Leu Ile Arg Gln Leu Ile Arg Leu Leu Thr Arg 755 760 765 Leu Tyr Ser Ile Cys Arg Asp Leu Leu Ser Arg Ser Phe Leu Thr Leu 770 775 780 Gln Leu Ile Tyr Gln Asn Leu Arg Asp Trp Leu Arg Leu Arg Thr Ala 785 790 795 800 Phe Leu Gln Tyr Gly Cys Glu Trp Ile Gln Glu Ala Phe Gln Ala Ala 805 810 815 Ala Arg Ala Thr Arg Glu Thr Leu Ala Gly Ala Cys Arg Gly Leu Trp 820 825 830 Arg Val Leu Glu Arg Ile Gly Arg Gly Ile Leu Ala Val Pro Arg Arg 835 840 845 Ile Arg Gln Gly Ala Glu Ile Ala Leu Leu 850 855 19 852 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of B_EHO lentiviral env protein 19 Met Ala His Val Asn Asn Tyr Leu Leu Val Thr Leu Leu Leu Ile Ser 1 5 10 15 Ile Tyr Gly Tyr Met Gly Lys Asn Phe Val Thr Val Phe Tyr Gly Ile 20 25 30 Pro Ala Trp Lys Asn Ala Ser Ile Pro Leu Phe Cys Ala Thr Arg Asn 35 40 45 Arg Asp Thr Trp Gly Thr Val Gln Cys Leu Pro Asp Asn Asp Asp Tyr 50 55 60 Thr Glu Ile Gln Leu Asn Ile Thr Glu Ala Phe Asp Ala Trp Asp Asn 65 70 75 80 Thr Val Thr Asp Gln Ala Thr Lys Asp Val Trp Ser Leu Phe Glu Thr 85 90 95 Ser Ile Lys Pro Cys Val Lys Leu Thr Pro Leu Cys Val Thr Met Lys 100 105 110 Cys Asn Lys Thr Trp Ser Ser Ala Ser Lys Glu Thr Thr Thr Ser Ser 115 120 125 Ala Ser Leu Arg Ser Ser Thr Gln Thr Leu Leu Asn Glu Asp Ser Lys 130 135 140 Cys Ile Gln Asn Asp Ser Cys Ala Gly Ile Gly Leu Glu Glu Met Ile 145 150 155 160 Asp Cys Gln Phe Lys Met Thr Gly Leu Lys Arg Asp Glu Ser Lys Gln 165 170 175 Tyr Lys Asp Thr Trp Tyr Lys Gln Asp Leu Val Cys Glu Lys Gly Thr 180 185 190 Arg Ser Asn Glu Ser Lys Cys Tyr Ile Lys Thr Cys Asn Thr Ser Ile 195 200 205 Ile Gln Glu Ser Cys Asp Lys His Tyr Trp Asp Ser Leu Arg Phe Arg 210 215 220 Tyr Cys Ala Pro Pro Gly Phe Ala Leu Leu Arg Cys Asn Asp Thr Lys 225 230 235 240 Tyr Ser Gly Phe Met Pro Asn Cys Ser Lys Val Val Val Ser Leu Tyr 245 250 255 Arg Met Met Glu Thr Gln Thr Ser Thr Trp Phe Gly Phe Asn Gly Thr 260 265 270 Arg Ala Glu Asn Arg Thr Tyr Ile Tyr Trp His Gly Lys Asp Asn Arg 275 280 285 Thr Ile Ile Ser Leu Asn Ser Tyr Tyr Asn Leu Thr Met His Cys Lys 290 295 300 Arg Pro Gly Asn Lys Met Val Val Pro Ile Arg Thr Val Ser Gly Ile 305 310 315 320 Leu Phe His Ser Gln Pro Ile Asn Lys Arg Pro Lys Gln Ala Trp Cys 325 330 335 Trp Phe Lys Gly Asn Trp Thr Glu Ala Ile Gln Glu Val Lys Glu Thr 340 345 350 Ile Lys Asn His Pro Arg Tyr Ser Gly Thr Thr Asn Ile Ser Gln Ile 355 360 365 Arg Leu Ala Glu His Ala Arg Ser Ser Asp Pro Glu Val Arg Tyr Met 370 375 380 Trp Thr Asn Cys Arg Gly Glu Phe Leu Tyr Cys Asn Met Thr Phe Phe 385 390 395 400 Leu Asn Trp Val Glu Asn Arg Thr Gly Leu Lys Arg Asn Tyr Ala Ser 405 410 415 Cys His Ile Arg Gln Ile Val Asn Thr Trp His Lys Ile Gly Arg Asn 420 425 430 Val Tyr Leu Pro Pro Arg Glu Gly Glu Leu Ser Cys Asn Ser Thr Val 435 440 445 Thr Ser Leu Ile Ala Asn Ile Asp Trp Ile Asp Lys Asn Leu Thr Asn 450 455 460 Ile Thr Val Ser Ala Glu Val Ser Glu Leu Tyr Lys Leu Glu Leu Gly 465 470 475 480 Asp Tyr Lys Leu Val Glu Ile Thr Pro Ile Gly Phe Ala Pro Thr Ser 485 490 495 Ile Lys Arg Tyr Ser Ser Val Thr Pro Arg Asn Lys Arg Gly Val Leu 500 505 510 Val Leu Gly Phe Leu Gly Phe Leu Ala Thr Ala Gly Ser Ala Met Gly 515 520 525 Ala Ala Ser Leu Thr Leu Ser Ala Gln Ser Arg Thr Leu Leu Ala Gly 530 535 540 Ile Val Gln Gln Gln Gln Gln Leu Val Asp Val Val Lys Arg Gln Gln 545 550 555 560 Glu Leu Leu Arg Leu Thr Val Trp Gly Thr Lys Asn Leu Gln Ala Arg 565 570 575 Val Thr Ala Ile Glu Lys Tyr Leu Lys Asp Gln Ala Gln Leu Asn Ser 580 585 590 Trp Gly Cys Ala Phe Arg Gln Val Cys His Thr Thr Val Pro Trp Val 595 600 605 Asn Glu Ser Leu Lys Pro Asp Trp Asn Asn Met Thr Trp Gln Gln Trp 610 615 620 Glu Arg Gln Val Arg Phe Leu Asp Ala Asn Ile Thr Lys Leu Leu Glu 625 630 635 640 Glu Ala Gln Ile Gln Gln Glu Lys Asn Met Tyr Glu Leu Gln Lys Leu 645 650 655 Asn Gln Trp Asp Ile Phe Ser Asn Trp Phe Asp Phe Thr Ser Trp Met 660 665 670 Ala Tyr Ile Arg Leu Gly Leu Tyr Ile Val Ile Gly Ile Val Val Leu 675 680 685 Arg Ile Ala Ile Tyr Ile Ile Gln Met Leu Ala Arg Leu Arg Lys Gly 690 695 700 Tyr Arg Pro Val Phe Ser Ser Pro Pro Ser Tyr Thr Gln Gln Ile Pro 705 710 715 720 Ile Arg Lys Asp Arg Gly Gln Pro Ala Asn Glu Glu Thr Glu Glu Gly 725 730 735 Gly Gly Asn Asn Glu Gly Tyr Arg Ser Trp Pro Trp Gln Ile Glu Tyr 740 745 750 Ile His Phe Pro Ile Arg Gln Leu Arg Asp Leu Leu Ile Trp Leu Tyr 755 760 765 Ser Gly Cys Arg Thr Leu Leu Ser Lys Thr Phe Gln Thr Leu Gln Pro 770 775 780 Val Leu Gln Pro Leu Arg Leu Pro Pro Ala Tyr Leu Arg Tyr Gly Ile 785 790 795 800 Ser Trp Phe Gln Glu Ala Ile Gln Ala Ala Ala Arg Ala Ala Gly Glu 805 810 815 Thr Leu Ala Ser Ala Ala Arg Thr Ser Trp Gly Val Leu Arg Arg Ala 820 825 830 Ala Gly Glu Ile Ile Ala Ile Pro Arg Arg Ile Arg Gln Gly Ala Glu 835 840 845 Leu Ala Leu Leu 850 20 877 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of SIVAGMVER3 lentiviral env protein 20 Met Lys Leu Thr Leu Leu Ile Gly Ile Leu Leu Ile Gly Ile Gly Val 1 5 10 15 Val Leu Asn Thr Arg Gln Gln Trp Val Thr Val Phe Tyr Gly Val Pro 20 25 30 Val Trp Lys Asn Ser Ser Val Gln Ala Phe Cys Met Thr Pro Thr Thr 35 40 45 Arg Leu Trp Ala Thr Thr Asn Ser Ile Pro Asp Asp His Asp Tyr Thr 50 55 60 Glu Val Pro Leu Asn Ile Thr Glu Pro Phe Glu Ala Trp Ala Asp Arg 65 70 75 80 Asn Pro Leu Val Ala Gln Ala Gly Ser Asn Ile His Leu Leu Phe Glu 85 90 95 Gln Thr Leu Lys Pro Cys Val Lys Leu Ser Pro Leu Cys Ile Lys Met 100 105 110 Ser Cys Val Glu Leu Asn Ser Ser Glu Pro Thr Thr Thr Pro Lys Ser 115 120 125 Thr Thr Ala Ser Thr Thr Asn Ile Thr Ala Ser Thr Thr Thr Leu Pro 130 135 140 Cys Val Gln Asn Lys Thr Ser Thr Val Leu Glu Ser Cys Asn Glu Thr 145 150 155 160 Ile Ile Glu Lys Glu Leu Asn Glu Glu Pro Ala Ser Asn Cys Thr Phe 165 170 175 Ala Met Ala Gly Tyr Val Arg Asp Gln Lys Lys Lys Tyr Ser Val Val 180 185 190 Trp Asn Asp Ala Glu Ile Met Cys Lys Lys Gly Asn Asn Ser Asn Arg 195 200 205 Glu Cys Tyr Met Ile His Cys Asn Asp Ser Val Ile Lys Glu Ala Cys 210 215 220 Asp Lys Thr Tyr Trp Asp Glu Leu Arg Leu Arg Tyr Cys Ala Pro Ala 225 230 235 240 Gly Phe Ala Leu Leu Lys Cys Asn Asp Tyr Asp Tyr Ala Gly Phe Lys 245 250 255 Thr Asn Cys Ser Asn Val Ser Val Val His Cys Thr Asn Leu Ile Asn 260 265 270 Thr Thr Val Thr Thr Gly Leu Leu Leu Asn Gly Ser Tyr Ser Glu Asn 275 280 285 Arg Thr Gln Ile Trp Gln Lys His Arg Val Ser Asn Asp Ser Val Leu 290 295 300 Val Leu Phe Asn Lys His Tyr Asn Leu Thr Val Thr Cys Lys Arg Pro 305 310 315 320 Gly Asn Lys Thr Val Leu Pro Val Thr Ile Met Ala Gly Leu Val Phe 325 330 335 His Ser Gln Arg Tyr Asn Thr Arg Leu Arg Gln Ala Trp Cys His Phe 340 345 350 Gln Gly Asn Trp Arg Gly Ala Trp Lys Glu Val Lys Asn Glu Ile Val 355 360 365 Lys Leu Pro Lys Asp Arg Tyr Gln Gly Thr Asn Asp Thr Glu Glu Ile 370 375 380 Tyr Leu Gln Arg Leu Phe Gly Asp Pro Glu Ala Ala Asn Leu Trp Phe 385 390 395 400 Asn Cys Gln Gly Glu Phe Phe Tyr Cys Lys Met Asp Trp Phe Leu Asn 405 410 415 Tyr Leu Asn Asn Arg Thr Val Asp Pro Asp His Asn Pro Cys Asn Gly 420 425 430 Thr Lys Gly Lys Gly Lys Ala Pro Gly Pro Cys Ala Gln Arg Thr Tyr 435 440 445 Val Ala Cys His Ile Arg Ser Val Ile Asn Asp Trp Tyr Thr Leu Ser 450 455 460 Arg Lys Thr Tyr Ala Pro Pro Arg Glu Gly His Leu Gln Cys Thr Ser 465 470 475 480 Thr Val Thr Gly Met Ser Val Glu Leu Asn Tyr Asn Ser Lys Asn Arg 485 490 495 Thr Asn Val Thr Leu Ser Pro Gln Ile Glu Thr Ile Trp Ala Ala Glu 500 505 510 Leu Gly Arg Tyr Lys Leu Val Glu Ile Thr Pro Ile Gly Phe Ala Pro 515 520 525 Thr Glu Val Arg Arg Tyr Thr Gly Gly His Asp Arg Thr Lys Arg Val 530 535 540 Pro Phe Val Leu Gly Phe Leu Gly Phe Leu Gly Ala Ala Gly Thr Ala 545 550 555 560 Met Gly Ala Ala Ala Thr Ala Leu Thr Val Gln Ser Gln His Leu Leu 565 570 575 Ala Gly Ile Leu Gln Gln Gln Lys Asn Leu Leu Ala Ala Val Glu Ala 580 585 590 Gln Gln Gln Met Leu Lys Leu Thr Ile Trp Gly Val Lys Asn Leu Asn 595 600 605 Ala Arg Val Thr Ala Leu Glu Lys Tyr Leu Glu Asp Gln Ala Arg Leu 610 615 620 Asn Ala Trp Gly Cys Ala Trp Lys Gln Val Cys His Thr Thr Val Pro 625 630 635 640 Trp Gln Trp Asn Asn Arg Thr Pro Asp Trp Asn Asn Met Thr Trp Leu 645 650 655 Glu Trp Glu Arg Gln Ile Ser Tyr Leu Glu Gly Asn Ile Thr Thr Gln 660 665 670 Leu Glu Glu Ala Arg Ala Gln Glu Glu Lys Asn Leu Asp Ala Tyr Gln 675 680 685 Lys Leu Ser Ser Trp Ser Asp Phe Trp Ser Trp Phe Asp Phe Ser Lys 690 695 700 Trp Leu Asn Ile Leu Lys Ile Gly Phe Leu Asp Val Leu Gly Ile Ile 705 710 715 720 Gly Leu Arg Leu Leu Tyr Thr Val Tyr Ser Cys Ile Ala Arg Val Arg 725 730 735 Gln Gly Tyr Ser Pro Leu Ser Pro Gln Ile His Ile His Pro Trp Lys 740 745 750 Gly Gln Pro Asp Asn Ala Glu Gly Pro Gly Glu Gly Gly Asp Lys Arg 755 760 765 Lys Asn Ser Ser Glu Pro Trp Gln Lys Glu Ser Gly Thr Ala Glu Trp 770 775 780 Lys Ser Asn Trp Cys Lys Arg Leu Thr Asn Trp Cys Ser Ile Ser Ser 785 790 795 800 Ile Trp Leu Tyr Asn Ser Cys Leu Thr Leu Leu Val His Leu Arg Ser 805 810 815 Ala Phe Gln Tyr Ile Gln Tyr Gly Leu Gly Glu Leu Lys Ala Ala Ala 820 825 830 Gln Glu Ala Val Val Ala Leu Ala Arg Leu Ala Gln Asn Ala Gly Tyr 835 840 845 Gln Ile Trp Leu Ala Cys Arg Ser Ala Tyr Arg Ala Ile Ile Asn Ser 850 855 860 Pro Arg Arg Val Arg Gln Gly Leu Glu Gly Ile Leu Asn 865 870 875 21 832 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of SIVSYK173 lentiviral env protein 21 Met Ala Ala Phe Arg Thr Tyr Ile Val Cys Leu Phe Ser Leu Ile Ser 1 5 10 15 Leu Gly Phe Met Glu Lys Gln Gln Tyr Val Thr Val Phe Tyr Gly Ile 20 25 30 Pro His Trp Glu Asp Ala Tyr Ala Pro Leu Phe Cys Thr Thr Ser His 35 40 45 Lys Gly Gly Trp Ala Thr Lys Asn Cys Val Pro Ser Ala Asp Gln Ile 50 55 60 Glu Val Arg Val Asn Ile Thr Gly Glu Tyr Phe Pro Ala Trp Asn Ser 65 70 75 80 Ser His Met Ile Arg Gln Gln Ile Leu Glu Asp Met Ser Ala Leu Phe 85 90 95 Leu Gln Ala Asn Arg Pro Cys Val Lys Leu Ala Pro Met Cys Ile Arg 100 105 110 Met Leu Cys Thr Leu Asp Asn Ser Pro Ala Thr Ser Thr Pro Thr Thr 115 120 125 Ser Pro Pro Thr Thr Pro Pro Asn Glu Thr Trp Trp Gly Asp Asn Ser 130 135 140 Thr Glu Pro Arg Phe Asn Cys Ser Phe Asn Leu Thr Gly Gly Phe Lys 145 150 155 160 Asp Lys Lys Gln Gln Tyr Arg Ala Phe Phe Tyr Lys Asp Asp Leu Met 165 170 175 Lys Glu Glu Gly Asn Ser Ser Tyr Tyr Tyr Leu Leu His Cys Asn Thr 180 185 190 Ser Val Ile Ser Ala Ala Cys Glu Lys Gln Thr Phe Gln Pro Phe Pro 195 200 205 Ile Gln Tyr Cys Ala Pro Pro Gly Tyr Ser Leu Leu Lys Cys Asn Asp 210 215 220 Thr Asn Phe Glu Gly Asp Asp Val Cys Thr Asn Val Thr Ala Val Ser 225 230 235 240 Cys Thr Gln Glu Phe Asn Thr Leu Ala Ser Thr Trp Phe Gln Leu Asn 245 250 255 Gly Thr Tyr Lys Ala Lys Asp Lys Val Arg Phe Ile Lys Gln Lys Asp 260 265 270 Lys Asn Glu Ser Val Ile Ile Leu Val Pro Glu Ala Leu Arg Leu Gln 275 280 285 Ile Ile Cys Glu Arg Pro Gly Asn Glu Ser Ile Lys Asn Ile Gln Leu 290 295 300 Ala Ala Gly Tyr Phe Leu Pro Val Ile Gln Gly Lys Leu Lys Thr Gly 305 310 315 320 Arg Asp Ala Lys Arg Ala Phe Cys Arg Val Thr Gly Asn Trp Thr Glu 325 330 335 Phe Phe Lys Gln Val His Glu Gln Ala Thr Lys Thr Trp Lys Asn Val 340 345 350 Thr Asn Thr Thr Trp Arg Ser Gln Pro Gly Gly Asp Leu Glu Val Arg 355 360 365 Thr His Trp Phe Gln Cys Gly Gly Glu Phe Phe Tyr Cys Asn Val Ser 370 375 380 Lys Leu Phe Ala Asn Ile Thr Asn Gly Asn Ala Ser Lys Asn Asn Tyr 385 390 395 400 Ala Ser Asn Leu Arg Leu Ser Cys Ala Ile Arg Gln Ile Ile Asn Asp 405 410 415 Trp Arg Tyr Val Arg Lys Leu Ile Tyr Leu Pro Pro Thr Ala Gly His 420 425 430 Ile Lys Cys Thr Ser Asn Val Thr Ala Val Leu Thr Asp Ile Glu Tyr 435 440 445 Tyr Pro Gly Ser Thr Leu Asn Phe Thr Pro Thr Ala Asn Val Glu Asp 450 455 460 Val Trp Arg Ala Asp Leu Phe Asn Tyr Lys Leu Ile Gln Ile Lys Pro 465 470 475 480 Ile Gly Phe Ala Pro Thr Asp Gln Arg Arg Tyr Glu Leu Pro Asn Thr 485 490 495 Arg Glu Lys Arg Ala Ala Pro Leu Ala Leu Gly Phe Leu Gly Leu Leu 500 505 510 Ser Ala Ala Gly Thr Ala Met Gly Gly Ala Ala Thr Ala Leu Thr Leu 515 520 525 Gln Ser Gln Thr Leu Leu Ala Gly Ile Val Gln Gln Gln Gln Lys Leu 530 535 540 Leu Glu Ala Val Glu Ala Gln Gln His Leu Leu Gly Leu Thr Val Trp 545 550 555 560 Gly Val Lys Asn Leu Asn Ala Arg Leu Thr Ala Leu Glu Thr Tyr Leu 565 570 575 Arg Asp Gln Ala Ile Leu Ser Asn Trp Gly Cys Ala Phe Lys Gln Ile 580 585 590 Cys His Thr Ala Val Thr Trp Glu Lys Ala Cys Gly Asn Asn Ser Asn 595 600 605 Phe Cys Pro Lys Pro Gln Trp Lys Asn Met Thr Trp His Arg Trp Glu 610 615 620 Gln Glu Val Asp Asn Leu Thr Asp His Ile Asp Gly Leu Leu Arg Glu 625 630 635 640 Ala Gln Glu Gln Gln Glu Arg Asn Val His Asp Leu Thr Lys Leu Gln 645 650 655 Glu Trp Asp Ser Leu Trp Ser Trp Phe Asp Leu Ser Lys Trp Phe Phe 660 665 670 Tyr Leu Lys Ile Gly Phe Tyr Val Ile Gly Ala Leu Val Leu Leu Arg 675 680 685 Leu Val Ser Phe Ser Val Gly Ile Ile Lys Asn Leu Leu Gly Gly Tyr 690 695 700 Val Pro Ile Leu Gln Asn Pro Thr Gln Gly Arg Lys Asp Pro Gly Lys 705 710 715 720 Pro Ala Asp Glu Glu Glu Gly Ser Gly Asp Arg Glu Gly Leu Asn Val 725 730 735 Ser Thr Phe Ser Arg Glu Ser Leu Arg Gln Ser Leu Glu Ala Gly Gln 740 745 750 Gln Leu Trp Arg Thr Val Cys Ser Ser Phe Arg Ser Leu Ile Arg Gln 755 760 765 Leu Thr Ile Thr Trp Gly Phe Ile Ser Tyr Gly Phe Asn Glu Leu Lys 770 775 780 Ile Ala Ala Ala Ser Leu Gly Arg Glu Ile Arg Asp Trp Val Ala Ala 785 790 795 800 Ile Trp Gln Ala Ile Tyr Ala Ala Thr Arg Arg Val Val Glu Ala Val 805 810 815 Ala Ala Leu Pro Arg Arg Leu Arg Gln Gly Leu Glu Ile Tyr Leu Asn 820 825 830 22 71 PRT Simian immunodeficiency virus Putative amino acid sequence of homologous region of extended rev ORF in SIVsmPbj1.9 22 Met Ser Ser Asn Glu Glu Glu Leu Arg Arg Arg Leu Arg Leu Ile His 1 5 10 15 Leu Leu His Gln Thr Ser Lys Tyr Gly Met Ser Trp Glu Ser Ala Ala 20 25 30 Tyr Arg Ala Leu Ala Ile Lys Cys Phe Arg Asp Leu Leu Cys Ser Ile 35 40 45 Cys Asn Ser Ile Leu Trp Tyr Thr Ser Met Glu Glu Cys Asp Ser Ser 50 55 60 Pro Leu Leu Cys Asn Gln Gly 65 70 23 75 PRT Simian immunodeficiency virus Putative amino acid sequence of homologous region of extended rev ORF in SIVrcmGB-1 23 Met Leu Pro Gly Gln Asp Glu Glu Asp Leu Arg Lys Lys Ile Arg Leu 1 5 10 15 Ile Asn Phe Leu Tyr Leu Ile Ser Lys Tyr Gly Val Pro Trp Thr Ser 20 25 30 Thr Ala Phe Arg Ala Ser Ala Lys Lys Val Phe Ile Asp Leu Leu Val 35 40 45 Thr Ile Ile Lys Gly Lys Tyr Asn Ser Leu Leu Trp Cys Pro Ser Met 50 55 60 Glu Lys Gln His Ser Ala Tyr Val Leu Cys Asp 65 70 75 24 71 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of extended rev ORF in SIVsmPbj 24 Met Ser Ser Asn Glu Glu Glu Leu Arg Arg Arg Leu Arg Leu Ile His 1 5 10 15 Leu Leu His Gln Thr Ser Lys Tyr Gly Met Ser Trp Glu Ser Ala Ala 20 25 30 Tyr Arg Ala Leu Ala Ile Lys Cys Phe Arg Asp Leu Leu Cys Ser Ile 35 40 45 Cys Asn Ser Ile Leu Trp Tyr Thr Ser Met Glu Glu Cys Asp Ser Ser 50 55 60 Pro Leu Leu Cys Asn Gln Glu 65 70 25 71 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of extended rev ORF in SIVsmM9 25 Met Ser Ser Asn Glu Glu Glu Leu Arg Arg Arg Leu Arg Leu Ile His 1 5 10 15 Phe Leu His Gln Thr Ser Lys Tyr Gly Met Ser Trp Glu Ser Ala Ala 20 25 30 Tyr Arg Ala Leu Ala Ile Lys Cys Phe Arg Asp Leu Leu Cys Ser Ile 35 40 45 Cys Asn Ser Ile Leu Trp Cys Thr Ser Met Glu Glu Cys Asp Ser Ser 50 55 60 Pro Leu Leu Cys Asn Gln Lys 65 70 26 71 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of extended rev ORF in SIVsmH4 26 Met Ser Ser Thr Glu Glu Glu Leu Arg Arg Arg Leu Arg Leu Ile His 1 5 10 15 Phe Leu His Gln Thr Ser Lys Tyr Gly Met Ser Trp Glu Ser Ala Ala 20 25 30 Tyr Arg Ala Leu Ala Ser Lys Cys Phe Arg Asp Leu Leu Cys Ser Ile 35 40 45 Cys Asn Ser Ile Leu Trp Cys Thr Ser Met Glu Glu Cys Asp Asn Ser 50 55 60 Pro Leu Leu Cys Asn Gln Glu 65 70 27 73 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of extended rev ORF in SIVmac142 27 Met Arg Ser His Thr Gly Glu Glu Glu Leu Arg Arg Arg Leu Arg Leu 1 5 10 15 Ile His Leu Leu His Gln Thr Ser Lys Tyr Gly Leu Ser Trp Lys Ser 20 25 30 Ala Ala Tyr Arg His Leu Ala Ser Lys Cys Leu Trp Asp Leu Leu Tyr 35 40 45 Ser Ile Cys His Ser Leu Leu Trp Cys Thr Ser Leu Glu Glu Cys Asp 50 55 60 Asn Ser Pro Leu Leu Cys Asn Gln Glu 65 70 28 73 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of extended rev ORF in SIVmac251 28 Met Ser Ser His Glu Arg Glu Glu Glu Leu Arg Lys Arg Leu Arg Leu 1 5 10 15 Ile His Leu Leu His Gln Thr Ser Lys Tyr Gly Met Ser Trp Glu Ser 20 25 30 Ala Ala Tyr Arg His Leu Ala Phe Lys Cys Leu Trp Asp Leu Leu Tyr 35 40 45 Ser Ile Cys His Ser Leu Leu Trp Cys Thr Ser Leu Glu Glu Cys Asp 50 55 60 Asn Ser Pro Leu Leu Cys Asn Gln Glu 65 70 29 73 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of extended rev ORF in SIVmac239 29 Met Ser Asn His Glu Arg Glu Glu Glu Leu Arg Lys Arg Leu Arg Leu 1 5 10 15 Ile His Leu Leu His Gln Thr Ser Lys Tyr Gly Met Ser Trp Glu Ser 20 25 30 Ala Ala Tyr Arg His Leu Ala Phe Lys Cys Leu Trp Asp Leu Leu Tyr 35 40 45 Ser Ile Cys His Ser Leu Leu Trp Cys Thr Ser Leu Glu Glu Cys Asp 50 55 60 Asn Ser Pro Leu Leu Cys Asn Gln Glu 65 70 30 73 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of extended rev ORF in SIVmac1all 30 Met Ser Ser His Glu Arg Glu Glu Glu Leu Arg Lys Arg Leu Arg Leu 1 5 10 15 Ile His Leu Leu His Gln Thr Ser Lys Tyr Gly Met Ser Trp Glu Ser 20 25 30 Ala Ala Tyr Arg His Leu Ala Phe Lys Cys Leu Trp Asp Leu Leu Tyr 35 40 45 Ser Ile Cys His Ser Leu Leu Trp Cys Thr Ser Leu Glu Glu Cys Asp 50 55 60 Asp Ser Pro Leu Leu Cys Asn Gln Glu 65 70 31 73 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of extended rev ORF in SIVmac132zm 31 Met Ser Asn His Glu Arg Glu Glu Glu Leu Arg Lys Arg Leu Arg Leu 1 5 10 15 Ile His Leu Leu His Gln Thr Ser Lys Tyr Gly Met Ser Trp Glu Ser 20 25 30 Ala Ala Tyr Arg His Leu Ala Phe Lys Cys Leu Trp Asp Leu Leu Tyr 35 40 45 Pro Ile Cys His Ser Leu Leu Trp Cys Thr Ser Leu Glu Glu Cys Asp 50 55 60 Asn Ser Pro Leu Leu Cys Asn Gln Glu 65 70 32 71 PRT Simian immunodeficiency virus Amino acid sequence of homologous region of extended rev ORF in SIVmacSTM 32 Met Ser Asp Gln Glu Glu Glu Leu Arg Lys Arg Leu Arg Leu Ile Gln 1 5 10 15 Phe Leu His Gln Thr Ser Lys Tyr Gly Leu Pro Trp Lys Ser Thr Ala 20 25 30 Tyr Arg Tyr Leu Ala Ile Lys Cys Leu Leu Asp Leu Leu His Ser Val 35 40 45 Cys His Gly Ile Leu Trp Cys Thr Ser Met Glu Glu Cys Asp Asp Ser 50 55 60 Pro Leu Leu Cys Asn Gln Glu 65 70 33 73 PRT Human immunodeficiency virus Amino acid sequence of homologous region of extended rev ORF in HIV2/FO784 33 Met Ser Gln Ala Glu Lys Glu Glu Glu Leu Arg Arg Arg Leu Arg Leu 1 5 10 15 Ile Tyr Leu Leu His Gln Thr Ser Lys His Gly Val Ser Trp Glu Ser 20 25 30 Ala Thr Tyr Arg Asn Leu Ala Ile Lys Tyr Phe Phe Asp Ile Leu Cys 35 40 45 Ser Val Cys His Ser Ile Leu Trp Tyr Thr Arg Met Glu Lys Cys Asp 50 55 60 Asn Thr Pro Leu Leu Arg Asn Gln Lys 65 70 34 73 PRT Human immunodeficiency virus 30, 47, 72 Amino acid sequence of homologous region of extended rev ORF in HIV2/BEN; Xaa = other = inactivating mutations 34 Met Ser Glu Arg Ala Asp Glu Glu Gly Leu Gln Gly Lys Leu Arg Leu 1 5 10 15 Leu Arg Leu Leu His Gln Thr Ser Glu Tyr Gly Ala Trp Xaa Glu Ser 20 25 30 Ala Val Cys Cys His Phe Thr Asn Lys Cys Leu Leu Ser Ile Leu Xaa 35 40 45 Pro Val Cys Asp Cys Phe Leu Trp His Thr Arg Val Glu Lys Cys Ile 50 55 60 Tyr Ser Leu Ile Leu Cys Asn Xaa Lys 65 70 35 74 PRT Human immunodeficiency virus 41, 73 Amino acid sequence of homologous region of extended rev ORF in HIV2/CAM2; Xaa = other = inactivating mutations 35 Met Thr Glu Arg Ala Asp Glu Glu Gly Leu Gln Arg Lys Leu Arg Leu 1 5 10 15 Ile Arg Leu Leu His Gln Thr Ser Glu Tyr Gly Ala Trp Gln Lys Ser 20 25 30 Ala Ala Tyr Cys His Ser Thr Ser Xaa Cys Leu Leu Asn Ile Leu Gln 35 40 45 Thr Thr Ile Cys Asp Cys Phe Leu Trp Arg Thr Arg Val Glu Lys Cys 50 55 60 Ile His Ser Pro Leu Leu Cys Asn Xaa Lys 65 70 36 72 PRT Human immunodeficiency virus 28, 29 Amino acid sequence of homologous region of extended rev ORF in HIV2/EHO; Xaa = other =inactivating mutations 36 Met Asn Ala Arg Glu Arg Asp Leu Gln Lys Gly Leu Arg Leu Leu His 1 5 10 15 Leu Leu His Gln Thr Ser Glu Tyr Gly Thr Cys Xaa Xaa Leu Pro Thr 20 25 30 Cys Tyr Thr Pro Ala Tyr Lys Tyr Leu Trp Val Tyr Gly Gln Glu Leu 35 40 45 Cys His Cys Leu Leu Trp Tyr Thr Arg Met Glu Lys Cys Ile Asn Ser 50 55 60 Pro Leu Leu Cys Tyr Gln Lys Gln 65 70 37 74 PRT Human immunodeficiency virus 26, 30, 41, 72 Amino acid sequence of homologous region of extended rev ORF in HIV2/GH1; Xaa = other =inactivating mutations 37 Met His Glu Lys Ala Asp Gly Glu Glu Leu Gln Glu Arg Leu Arg Leu 1 5 10 15 Ile Arg Leu Leu His Gln Thr Ser Glu Xaa Asp Val Trp Xaa Glu Ser 20 25 30 Thr Met Cys Cys Gln Leu Ala Ser Xaa Cys Leu Leu Ser Ile Leu His 35 40 45 Pro Ile Cys Asp Cys Phe Leu Trp Arg Ala Arg Val Glu Lys Cys Ile 50 55 60 His Ser Pro Leu Leu Cys Asn Xaa Lys Gln 65 70 38 73 PRT Human immunodeficiency virus 29, 30, 41 Amino acid sequence of homologous region of extended rev ORF in HIV2/KR; Xaa = other = inactivating mutations 38 Met Asn Gly Arg Ala Asp Glu Glu Gly Leu Gln Arg Lys Gln Arg Leu 1 5 10 15 Ile Arg Leu Leu His Gln Thr Ser Glu Tyr Asn Gly Xaa Xaa Lys Ser 20 25 30 Ala Asn Cys Cys His Phe Thr Asn Xaa Cys Leu Leu Asn Ile Leu Arg 35 40 45 Pro Ile Cys Asp Cys Phe Leu Trp His Thr Arg Val Glu Glu Cys Ile 50 55 60 His Ser Pro Leu Leu Cys Asn Gln Lys 65 70 39 75 PRT Human immunodeficiency virus 41 Amino acid sequence of homologous region of extended rev ORF in HIV2/MDS; Xaa = other = inactivating mutation 39 Met Asn Glu Arg Ala Asp Glu Glu Gly Leu Gln Arg Lys Leu Arg Leu 1 5 10 15 Ile Arg Leu Leu His Gln Thr Ser Glu Tyr Asp Ala Gln Asn Ala Ser 20 25 30 Ala Ala Tyr Cys His Phe Thr Asn Xaa Cys Leu Leu Asn Ile Leu Gln 35 40 45 Thr Thr Thr Ile Cys Asn Cys Phe Leu Trp His Thr Arg Val Glu Glu 50 55 60 Cys Ile His Ser Pro Leu Leu Cys Asn Gln Lys 65 70 75 40 73 PRT Human immunodeficiency virus 29, 30, 41 Amino acid sequence of homologous region of extended rev ORF in HIV2/NIHZ; Xaa = other =inactivating mutations 40 Met Thr Glu Arg Ala Asp Glu Glu Gly Leu Gln Arg Lys Leu Arg Leu 1 5 10 15 Ile Arg Leu Leu His Gln Thr Ser Glu Tyr Glu Gly Xaa Xaa Glu Ser 20 25 30 Thr Ala Asp Cys Tyr Cys Thr Ser Xaa Cys Leu Pro Asn Thr Leu Gln 35 40 45 Ala Ile Cys Asp Cys Phe Leu Arg His Thr Arg Val Glu Glu Cys Ile 50 55 60 His Ser Pro Val Leu Cys Asn Gln Lys 65 70 41 69 PRT Human immunodeficiency virus 38 Amino acid sequence of homologous region of extended rev ORF in HIV2/ROD; Xaa = other = inactivating mutations 41 Met Asn Glu Arg Ala Asp Glu Glu Gly Leu Gln Arg Lys Leu Arg Leu 1 5 10 15 Ile Arg Leu Leu His Gln Thr Ser Glu Tyr Asp Glu Ser Ala Ala Tyr 20 25 30 Cys His Phe Ile Ser Xaa Cys Leu Leu Ser Ile Leu His Pro Ile Cys 35 40 45 Asn Cys Phe Leu Trp Thr His Val Glu Lys Cys Asn His Ser Pro Leu 50 55 60 Leu Cys Asn Gln Lys 65 42 73 PRT Human immunodeficiency virus 30, 41, 72 Amino acid sequence of homologous region of extended rev ORF in HIV2/SBLISY; Xaa = other = inactivating mutations 42 Met Thr Glu Arg Ala Asp Glu Glu Gly Val Arg Arg Lys Leu Arg Leu 1 5 10 15 Ile Arg Leu Leu His Gln Thr Ser Glu Tyr Asn Glu Trp Xaa Asn Ser 20 25 30 Ala Ala Cys Cys Leu Ser Ala Asn Xaa Cys Leu Leu Asn Ile Leu His 35 40 45 Gln Ile Cys Asp Cys Phe Leu Trp Ser Thr Arg Val Glu Lys Cys Ile 50 55 60 His Ser Pro Leu Leu Cys Asn Xaa Lys 65 70 43 73 PRT Human immunodeficiency virus 26, 30, 41, 72 Amino acid sequence of homologous region of extended rev ORF in HIV2/ST; Xaa = other = inactivating mutations 43 Met Asn Glu Arg Ala Glu Glu Glu Glu Leu Arg Arg Lys Leu Arg Leu 1 5 10 15 Ile Arg Leu Leu His Gln Thr Ser Glu Xaa Asp Val Trp Xaa Glu Ser 20 25 30 Thr Ile Cys Cys Gln Leu Ala Ser Xaa Cys Leu Leu Asn Ile Leu Arg 35 40 45 Pro Ile Cys Asp Cys Phe Leu Trp Arg Ala Arg Val Glu Lys Cys Ile 50 55 60 His Ser Pro Leu Leu Cys Asn Xaa Lys 65 70 44 74 PRT Human immunodeficiency virus 28, 47 Amino acid sequence of homologous region of extended rev ORF in HIV2/UC1; Xaa = other = inactivating mutations 44 Met Thr Thr Arg Glu Lys Asp Leu Gln Lys Gly Leu Arg Leu Leu His 1 5 10 15 Leu Leu His Gln Thr Ser Glu Tyr Gly Thr His Xaa Gln Ser Pro Val 20 25 30 Tyr Phe Ala Pro Thr Tyr Lys Cys Leu Trp Val Ser Gly Ser Xaa Glu 35 40 45 Lys Leu Cys His Cys Leu Leu Trp His Thr Cys Met Glu Glu Arg Asn 50 55 60 Gly Ser Ser Leu Leu Cys Asn His Lys Gln 65 70 45 518 PRT Simian immunodeficiency virus Deduced amino acid sequence of SIVrcm Gag protein 45 Met Gly Ala Arg Ala Ser Leu Leu Ser Gly Lys Lys Leu Asp Ala Trp 1 5 10 15 Glu Ser Val Arg Leu Arg Pro Gly Gly Lys Lys Lys Tyr Met Leu Lys 20 25 30 His Leu Val Trp Ala Cys Lys Lys Leu Asn Lys Phe Gly Leu Ser Asp 35 40 45 His Leu Leu Glu Thr Ala Thr Gly Cys Glu Lys Ile Leu Gly Val Leu 50 55 60 Leu Pro Leu Val Pro Thr Gly Ser Glu Gly Leu Lys Ser Leu Phe Asn 65 70 75 80 Leu Cys Cys Val Leu Trp Cys Val His Lys Glu Val Lys Val Lys Asp 85 90 95 Thr Glu Glu Ala Val Ala Lys Val Lys Glu Cys Cys His Leu Val Glu 100 105 110 Lys Ala Glu Asn Thr Thr Glu Lys Glu Lys Gly Ala Thr Ala Pro Pro 115 120 125 Ser Gly Gln Arg Gly Asn Tyr Pro Ile Ile Thr Ile Asn Gln Gln Pro 130 135 140 Glu His Asn Pro Ile Ser Pro Arg Thr Leu Asn Ala Trp Val Lys Val 145 150 155 160 Val Glu Glu Lys Lys Phe Ser Ala Glu Val Ala Pro Met Phe Ser Ala 165 170 175 Leu Ser Glu Gly Cys Ile Pro Tyr Asp Ile Asn Gln Met Leu Asn Ala 180 185 190 Ile Gly Glu His Gln Gly Ala Leu Gln Ile Val Lys Glu Val Ile Asn 195 200 205 Glu Glu Ala Ala Asp Trp Asp Ala Arg His Pro Val Pro Gly Pro Ile 210 215 220 Pro Ala Gly Gln Leu Arg Glu Pro Thr Gly Ser Asp Ile Ala Gly Thr 225 230 235 240 Thr Ser Ser Ile Ala Glu Gln Ile Ala Trp Thr Thr Arg Ala Asn Asn 245 250 255 Pro Ile Asn Val Gly Asn Leu Tyr Arg Asn Trp Ile Ile Val Gly Leu 260 265 270 Gln Lys Trp Val Lys Met Tyr Asn Pro Val Asn Ile Leu Asp Ile Lys 275 280 285 Gln Gly Pro Lys Glu Ser Phe Lys Asp Tyr Val Asp Arg Phe Tyr Lys 290 295 300 Ala Leu Arg Ala Glu Gln Ala Asp Pro Ala Val Lys Asn Trp Met Thr 305 310 315 320 Gln Ser Leu Leu Ile Gln Asn Ala Asn Pro Asp Cys Lys Met Val Leu 325 330 335 Lys Gly Leu Gly Met Asn Pro Ser Leu Glu Glu Met Leu Thr Ala Cys 340 345 350 Gln Gly Val Gly Gly Pro Gln His Lys Ala Arg Val Leu Ala Glu Ala 355 360 365 Met Gln Met Met Gln Ser Asn Ile Met Ala Gln Gln Ser Ala Asn Arg 370 375 380 Gly Pro Pro Arg Arg Ser Gly Gly Asn Pro Asn Leu Arg Cys Tyr Asn 385 390 395 400 Cys Gly Lys Pro Gly His Ile Ser Arg Tyr Cys Lys Ala Pro Arg Arg 405 410 415 Lys Gly Cys Trp Lys Cys Gly Ser Pro Asp His Leu Leu Lys Asp Cys 420 425 430 Thr Lys Gln Ile Asn Phe Leu Gly Arg Leu Pro Trp Gly Gln Gly Lys 435 440 445 Pro Arg Asn Phe Pro Leu Thr Ser Leu Thr Pro Ser Ala Pro Gly Met 450 455 460 Glu Ser Asn Tyr Asp Pro Ala Glu Glu Met Leu Lys Asn Tyr Leu Arg 465 470 475 480 Arg Ala Gly Glu Gln Lys Arg Gln Gln Arg Gln Glu Glu Ser Lys Lys 485 490 495 Arg Glu Gly Ala Tyr Gln Glu Ala Leu Thr Ser Leu Asn Ser Leu Phe 500 505 510 Gly Ser Asp Gln Leu Gln 515 46 1018 PRT Simian immunodeficiency virus Deduced amino acid sequence of SIVrcm Pol protein 46 Phe Phe Arg Glu Thr Pro Leu Gly Ser Gly Glu Ala Glu Glu Leu Ser 1 5 10 15 Phe Asp Phe Leu Asp Ser Leu Cys Ser Arg Asp Gly Glu Gln Leu Arg 20 25 30 Pro Cys Arg Arg Asp Ala Lys Glu Leu Ser Glu Glu Gly Arg Gly Thr 35 40 45 Lys Glu Thr Thr Glu Ala Gly Arg Glu Gln Glu Glu Arg Gly Ser Ile 50 55 60 Ser Gly Ser Leu Asn Leu Pro Gln Phe Ala Leu Trp Lys Arg Pro Thr 65 70 75 80 Thr Ile Ala Gln Ile Glu Gly Gln Lys Val Glu Val Leu Leu Asp Thr 85 90 95 Gly Ala Asp Asp Thr Val Ile Glu Gly Ile Glu Leu Gly Asn Asp Trp 100 105 110 Thr Pro Lys Ile Ile Gly Gly Ile Gly Gly Tyr Ile Asn Val Lys Gln 115 120 125 Tyr Lys Asn Cys Glu Ile Glu Ile Ala Gly Lys Arg Thr His Ala His 130 135 140 Val Leu Val Gly Pro Thr Pro Val Asn Ile Ile Gly Arg Asn Val Leu 145 150 155 160 Lys Lys Leu Gly Ala Thr Leu Asn Phe Pro Ile Ser Gln Ile Glu Thr 165 170 175 Ile Lys Val Glu Leu Lys Ser Gly Gln Asp Gly Pro Arg Val Lys Gln 180 185 190 Trp Pro Leu Ser Lys Glu Lys Ile Glu Ala Leu Thr Glu Ile Cys Asn 195 200 205 Ala Met Glu Lys Glu Gly Lys Ile Ser Lys Ile Gly Pro Glu Asn Pro 210 215 220 Tyr Asn Thr Pro Ile Phe Cys Ile Lys Lys Lys Asp Ser Thr Lys Trp 225 230 235 240 Arg Lys Leu Val Asp Phe Arg Glu Leu Asn Lys Arg Thr Gln Asp Phe 245 250 255 Phe Glu Val Gln Leu Gly Ile Pro His Pro Gly Gly Leu Lys Gln Cys 260 265 270 Glu Arg Ile Thr Val Leu Asp Ile Gly Asp Ala Tyr Phe Ser Cys Leu 275 280 285 Leu Tyr Glu Pro Phe Arg Lys Tyr Thr Ala Phe Thr Ile Pro Ala Val 290 295 300 Asn Asn Gln Gly Pro Gly Val Arg Tyr Gln Tyr Asn Val Leu Pro Gln 305 310 315 320 Gly Trp Lys Gly Ser Pro Ala Ile Phe Gln Ala Ser Ala Asn Lys Ile 325 330 335 Leu Gln Pro Phe Arg Glu Glu Asn Pro Asp Val Ile Ile Tyr Gln Tyr 340 345 350 Met Asp Asp Leu Phe Val Gly Ser Asp Arg Thr Lys Leu Glu His Asp 355 360 365 Lys Met Ile Lys Gln Leu Arg Asp His Leu Leu Phe Trp Gly Phe Glu 370 375 380 Thr Pro Asp Lys Lys Phe Gln Asp Lys Pro Pro Tyr Leu Trp Met Gly 385 390 395 400 Tyr Glu Leu His Pro Lys Ser Trp Thr Val Gln Glu Ile Lys Leu Pro 405 410 415 Glu Lys Glu Glu Trp Thr Val Asn Asp Ile Gln Lys Leu Val Gly Lys 420 425 430 Leu Asn Trp Ala Ser Gln Ile Tyr Ser Gly Leu Arg Thr Lys Glu Leu 435 440 445 Cys Lys Leu Ile Arg Gly Ala Lys Ala Leu Asp Glu Lys Val Glu Met 450 455 460 Thr Lys Glu Ala Glu Ile Glu Tyr Glu Glu Asn Lys Met Ile Leu Lys 465 470 475 480 Glu Lys Leu His Gly Val Tyr Tyr Asp Glu Lys Lys Pro Leu Val Ala 485 490 495 Asn Ile Gln Lys Leu Glu Gly Gly Gln Trp Ser Tyr Gln Ile Glu Gln 500 505 510 Glu Ser Gly Lys Pro Leu Lys Thr Gly Lys Tyr Ala Lys Gln Lys Thr 515 520 525 Ala His Thr Asn Glu Ile Arg Met Leu Ala Gly Leu Val Gln Lys Ile 530 535 540 Ala Lys Glu Ala Ile Val Ile Trp Gly Arg Leu Pro Thr Phe Arg Leu 545 550 555 560 Pro Ile Glu Arg Glu Val Trp Asp Trp Arg Ser Gln Tyr Trp Gln Val 565 570 575 Thr Trp Ile Pro Asp Trp Glu Phe Val Ser Thr Pro Pro Leu Ile Arg 580 585 590 Leu Gly Tyr Asn Leu Val Lys Asp Pro Ile Pro Gly Glu Glu Val Tyr 595 600 605 Tyr Val Asp Gly Ala Ala Asn Arg Asn Ser Lys Ile Gly Lys Ala Gly 610 615 620 Tyr Val Thr Asn Arg Gly Lys Glu Lys Val Lys Glu Leu Glu Glu Thr 625 630 635 640 Thr Asn Gln Lys Ala Glu Leu Glu Ala Val Leu Leu Ala Leu Lys Asp 645 650 655 Ser Gly Pro Lys Val Asn Ile Val Thr Asp Ser Gln Tyr Val Tyr Gly 660 665 670 Ile Leu Glu Ala Gln Pro Asp Thr Ser Asp Ser Gly Leu Val Thr Glu 675 680 685 Ile Ile Asn Gln Met Ile Gly Lys Glu Ala Val Tyr Leu Ser Trp Val 690 695 700 Pro Ala His Lys Gly Ile Gly Gly Asn Glu Glu Val Asp Lys Leu Val 705 710 715 720 Ser Lys Gly Ile Arg Gln Val Leu Phe Leu Asp Gly Ile Glu Lys Ala 725 730 735 Gln Glu Glu His Glu Lys Tyr His Asn Asn Trp Arg Ala Leu Ala Glu 740 745 750 Asp Phe Gln Ile Pro Gln Ile Val Ala Lys Glu Ile Val Ala Gln Cys 755 760 765 Pro Lys Cys Gln Val Lys Gly Glu Ala Ile His Gly Gln Val Asp Ala 770 775 780 Ser Pro Gly Thr Trp Gln Met Asp Cys Thr His Leu Glu Gly Lys Ile 785 790 795 800 Ile Ile Val Ala Val His Val Ala Ser Gly Tyr Ile Glu Ala Glu Val 805 810 815 Ile Pro Ala Glu Thr Gly Lys Glu Thr Ala His Phe Leu Leu Lys Leu 820 825 830 Ala Ala Arg Trp Pro Val Arg Lys Leu His Thr Asp Asn Gly Ala Asn 835 840 845 Phe Thr Ser Ala Ala Val Gln Ala Val Cys Trp Trp Ala Gln Ile Glu 850 855 860 His Ala Phe Gly Val Pro Tyr Asn Pro Gln Ser Gln Gly Val Val Glu 865 870 875 880 Ser Met Asn Lys Gln Leu Lys Ile Ile Ile Glu Gln Val Arg Glu Gln 885 890 895 Ala Glu Lys Leu Glu Thr Ala Val Gln Met Ala Val Leu Val His Asn 900 905 910 Phe Lys Arg Lys Gly Gly Ile Gly Gly Tyr Ser Ala Gly Glu Arg Ile 915 920 925 Ile Asp Ile Ile Ala Thr Asp Leu Ala Thr Asn Lys Leu Gln Asn Gln 930 935 940 Ile Ser Lys Ile Gln Asn Phe Arg Val Tyr Tyr Arg Glu Gly Arg Asp 945 950 955 960 Gln Leu Trp Arg Gly Pro Ala Lys Leu Ile Trp Lys Gly Glu Gly Ala 965 970 975 Val Val Ile Gln Glu Glu Thr Gly Asp Leu Lys Val Val Pro Arg Arg 980 985 990 Lys Ala Lys Ile Ile Lys Glu Tyr Gly Arg Lys Asp Val Asp Ser Glu 995 1000 1005 Ala Asn Leu Ala Gly Arg Gln Glu Glu Asn 1010 1015 47 216 PRT Simian immunodeficiency virus Deduced amino acid sequence of SIVrcm Vif protein 47 Met Ala Glu Lys Met Trp Ile Val Arg Pro Ile Trp Arg Val Asp Arg 1 5 10 15 Arg Lys Ile Glu Gln Trp His Ser Leu Val Lys Tyr His Gln Tyr Lys 20 25 30 Gly Lys Lys Ala Ala Lys Glu Trp Glu Tyr Val Pro His Phe Lys Val 35 40 45 Pro Trp Gly Trp Trp Ser His Ser Glu Val His Ile Pro Leu Glu Glu 50 55 60 Gly Ser Lys Leu Lys Ile Thr Thr Tyr Trp Asn Leu Thr Val Glu Lys 65 70 75 80 Gly Trp Leu Gly Thr Tyr Gly Val Gly Ile Leu Trp Ile Lys Gly Asp 85 90 95 Tyr Val Thr Asp Val Phe Pro Trp Thr Ala Asp Ser Leu Ile His Lys 100 105 110 Ile Tyr Phe Pro Cys Phe Thr Asp Arg Ala Ile Arg Gln Ser Leu Leu 115 120 125 Gly Glu Lys Val Leu Val Cys Ala Phe Gln Gly Gly His Arg Asp Gln 130 135 140 Val Gly Thr Leu Gln Phe Leu Ala Ile Gln Ala Trp Ala Lys Ser Gln 145 150 155 160 Leu Asp Arg Tyr Gly Arg Lys Ser Pro Arg Gly Pro His Trp Gly Trp 165 170 175 Arg Ser Arg Val Pro Ala Leu Ala Thr Gly His Ala Arg Lys Gly Gln 180 185 190 Leu Gly Ser Gln Val Thr Leu Ser Ser Arg Val His Phe Pro Ser Val 195 200 205 Ala His Leu Cys Gly Thr Leu Ala 210 215 48 104 PRT Simian immunodeficiency virus Deduced amino acid sequence of SIVrcm Vpx protein 48 Met Ala Glu Arg Ala Pro Glu Val Pro Thr Gly Ala Gly Glu Ala Glu 1 5 10 15 Phe Gln Pro Trp Leu Arg Asp Met Leu Glu Lys Val Asn Leu Glu Ala 20 25 30 Arg Leu His Phe His Pro Glu Phe Ile Phe Arg Leu Trp Arg Thr Cys 35 40 45 Val Glu His Trp His Asp Val His Gln Arg Ser Leu Glu Tyr Ala Ala 50 55 60 Tyr Arg Tyr Leu Leu Leu Met Gln Lys Ala Leu Phe Ile His Cys Gln 65 70 75 80 Thr Gly Cys Ser Gln Arg His Gly Pro Asn Pro Arg Ala Val Gly Glu 85 90 95 Arg Ile Thr Ile Leu Pro Gly Met 100 49 100 PRT Simian immunodeficiency virus Deduced amino acid sequence of SIVrcm Vpr protein 49 Met Glu Leu Pro Pro Glu Asp Glu Gly Pro Gln Arg Glu Pro Tyr Asp 1 5 10 15 Glu Trp Leu Met Asp Thr Leu Ile Glu Leu Gln Glu Glu Ala Lys Lys 20 25 30 His Phe Thr Tyr Ala Leu Leu Thr Gln Ile Gly Asp Tyr Val Tyr Glu 35 40 45 Gln His Gly Asp Ser Ile Glu Gly Val Gln Ala Met Ile Arg Leu Leu 50 55 60 Gln Arg Ala Leu Phe Leu His Phe Arg Asn Gly Cys Ala Gly Ser Arg 65 70 75 80 Ile Gly Thr Ser Arg Gly Ser Asn Pro Leu Arg Ser Ile Pro Gln Thr 85 90 95 Arg Asn Ile Met 100 50 106 PRT Simian immunodeficiency virus Deduced amino acid sequence of SIVrcm Tat protein 50 Met Asp Val Gln Gly Val Gly Leu Glu His Pro Glu Glu Val Ile Leu 1 5 10 15 Tyr Asp Pro Phe Arg Lys Arg Glu Thr Ser Cys Asn Thr Cys Tyr Cys 20 25 30 Lys Lys Cys Cys Tyr His Cys Gln Leu Cys Phe Leu Gln Lys Gly Leu 35 40 45 Gly Ile Asn Tyr Ala Ser Arg Ala Arg Arg Arg Arg Ser Lys Glu Glu 50 55 60 Asn Lys Ala Asp Lys Phe Pro Val Pro Asn His Arg Ser Ile Ser Thr 65 70 75 80 Thr Arg Gly Asn Arg Lys Leu Gln Glu Lys Lys Glu Lys Thr Val Glu 85 90 95 Lys Lys Val Ala Thr Ser Thr Thr Ile Gly 100 105 51 94 PRT Simian immunodeficiency virus Deduced amino acid sequence of SIVrcm Rev protein 51 Met Leu Pro Gly Gln Asp Glu Glu Asp Leu Arg Lys Lys Ile Arg Leu 1 5 10 15 Ile Asn Phe Leu Tyr Leu Ile Thr Asp Pro Tyr Pro Gln His Gly Gly 20 25 30 Thr Ala Asn Ser Arg Arg Lys Lys Arg Arg Arg Trp Arg Arg Arg Trp 35 40 45 Gln Gln Val Gln Gln Leu Ala Glu Arg Ile Leu Leu Asp Ser Thr Asp 50 55 60 Pro Pro Val Glu Gln Asp Leu Asp Ala Ala Ile Ala Asp Leu Gln Lys 65 70 75 80 Leu Gln Leu Asn Asn Leu Pro Glu Pro Pro Val Asp Phe Ser 85 90 52 850 PRT Simian immunodeficiency virus Deduced amino acid sequence of SIVrcm Env protein 52 Met Asp Lys Lys Leu Val Ile Val Leu Ile Val Val Ile Gly Ile Ile 1 5 10 15 Leu Val Gln Gly Ser Gln Lys Pro Gln Tyr Ile Thr Val Phe Tyr Gly 20 25 30 Val Pro Val Trp Arg Asn Ser Thr Val Pro Met Phe Cys Val Thr Asp 35 40 45 Asn Thr Gln Ser Trp Gly Thr Leu Asn Cys Ile Pro Glu Gly Gly Ile 50 55 60 Ser Pro Glu Val Ser Ile Asn Val Ser Glu Arg Phe Asp Ala Trp Asn 65 70 75 80 Asn Ser Leu Tyr Glu Gln Ala Lys Asp Asn Val Trp Asn Leu Tyr Asp 85 90 95 Ser Thr Leu Lys Pro Cys Val Arg Leu Ser Pro Leu Cys Ile Thr Met 100 105 110 Asn Cys Ser Ala Ile Asn Gly Ser Trp Asp Gly Ile Pro Thr Ser Ala 115 120 125 Pro Pro Thr Thr Thr Lys Thr Thr Thr Gln Arg Thr Ile Gly Val Glu 130 135 140 Lys Glu Cys Thr Ala Gly Asn Glu Thr Cys Glu Glu Val Gln Asp Ala 145 150 155 160 Asp Val Met Ser Cys Glu Phe Ala Val Ala Gly Leu Lys Arg Asp Glu 165 170 175 Lys His Lys Tyr Asn Asp Thr Trp Tyr Ser Arg Asp Leu Trp Cys Glu 180 185 190 Lys Glu Thr Asn Ser Thr Asn Ser Thr Lys Lys Lys Cys Phe Val Arg 195 200 205 His Cys Asn Thr Thr Ser Ile Gln Gln Phe Cys Glu Pro Lys Tyr Trp 210 215 220 Glu Pro Phe Arg Leu Arg Tyr Cys Ala Pro Pro Gly Phe Ala Leu Leu 225 230 235 240 Val Cys Lys Asp Lys Asn Tyr Thr Gly Phe Asp Thr Cys Val Asn Val 245 250 255 Thr Ala Thr Ser Cys Thr His Met Ile Asn Thr Thr Val Ala Ser Gly 260 265 270 Phe Gly Leu Asn Gly Ser Ile Asn Val Asn Glu Thr Trp Ile Tyr Gln 275 280 285 Arg Arg Gln Ser Asn Arg Thr Val Ile Gly Leu Asn Ser Phe Tyr Asn 290 295 300 Leu Ser Val Thr Cys Arg Arg Pro Ser Asn Arg Thr Val Lys Gly Ile 305 310 315 320 Ser Leu Ala Thr Gly Val Phe Ile Ser Leu Arg Val Glu Lys Arg Pro 325 330 335 Lys Gly Ala Trp Cys Arg Phe Glu Gly Asn Trp Thr Asp Ala Trp Lys 340 345 350 Glu Val Lys Glu Arg Val Lys Thr Thr Lys Gly Tyr Arg Gly Thr Ser 355 360 365 Asn Thr Asp Lys Ile Lys Ile Arg Thr Val Tyr Gly Gly Asp Asp Glu 370 375 380 Ala Arg Tyr Phe Trp Leu Asn Cys Asn Gly Glu Phe Leu Tyr Cys Lys 385 390 395 400 Leu Asn Trp Phe Leu Asn Leu Leu Asn Asn Glu Thr Val Gly Thr Thr 405 410 415 Asn Glu Lys Arg Lys Ala Pro Phe Val Pro Cys Ile Thr Lys Met Ile 420 425 430 Val Asn Asp Trp Tyr Thr Val Ser Arg Lys Val Tyr Thr Pro Pro Arg 435 440 445 Pro Asp Ala Leu Lys Cys Ser Ala Gln Val Ser Tyr Leu Leu Ala Asp 450 455 460 Ile Asp Tyr Ile Asn Asp Ser Glu Thr Asn Ile Thr Leu Ser Ala Glu 465 470 475 480 Val Gly Asp Tyr Trp Ala Ala Glu Leu Gly Arg Tyr Lys Ala Ile Glu 485 490 495 Ile Arg Pro Ile Gly Phe Ala Pro Thr Glu Ile Lys Arg Tyr Gln Thr 500 505 510 Lys Gln Lys Arg Val Pro Leu Val Leu Gly Phe Leu Gly Phe Leu Ser 515 520 525 Ala Ala Gly Thr Ala Met Gly Ala Ala Ala Thr Ala Leu Thr Val Gln 530 535 540 Ser Arg His Leu Leu Ala Gly Ile Leu Gln Gln Gln Lys Asn Leu Leu 545 550 555 560 Asp Ile Val Lys Arg Gln Gln Asn Leu Leu Lys Leu Thr Val Trp Gly 565 570 575 Thr Lys Asn Leu Gln Ala Arg Val Thr Ala Ile Glu Lys Tyr Leu Ala 580 585 590 Asp Gln Ser Leu Leu Asn Thr Phe Gly Cys Ala Trp Arg Gln Val Cys 595 600 605 His Thr Val Val Pro Trp Thr Phe Asn Lys Thr Pro Glu Trp Gln Lys 610 615 620 Glu Ser Trp Leu Gln Trp Glu Arg Asn Ile Ser Tyr Leu Glu Ala Asn 625 630 635 640 Ile Thr Ile Ala Leu Gln Glu Ala Gln Asp Gln His Glu Lys Asn Val 645 650 655 His Glu Leu Glu Lys Leu Ser Asn Trp Gly Asp Ala Phe Ser Trp Leu 660 665 670 Asn Leu Asp Trp Trp Met Gln Tyr Ile Lys Ile Gly Phe Phe Ile Val 675 680 685 Ile Gly Ile Ile Gly Leu Arg Val Ala Trp Leu Leu Trp Asn Cys Leu 690 695 700 Ser Asn Leu Arg Gln Gly Tyr Arg Pro Leu Ser Pro Pro Ser Tyr Val 705 710 715 720 Gln Gln Ile His Ile His Asn Thr Gly Glu Pro Gln Thr Pro Gly Glu 725 730 735 Lys Arg Glu Asp Gly Gly Glu Glu Gly Gly Asn Lys Tyr Asn Asn Trp 740 745 750 Leu Arg Glu Tyr Cys Trp Ile Gln Leu Ile His Pro Leu Ser Arg Ile 755 760 765 Trp Thr Gln Leu Ser Gln Ile Cys Arg Ser Cys Ser Ser Ile Ile Phe 770 775 780 Gln Ser Leu Arg Trp Ile Leu Ala Lys Ile Gln Tyr Gly Trp Gln Glu 785 790 795 800 Phe Lys Glu Phe Ser Ser Trp Phe Ala Glu Met Ala Leu Gln Asn Ala 805 810 815 Tyr Tyr Thr Trp Arg Gly Leu Cys Ala Val Ala Arg Asp Phe Ala Gly 820 825 830 Trp Pro Ala Met Val Cys Arg Arg Ile Arg Gln Gly Leu Glu Arg Leu 835 840 845 Cys Asn 850 53 224 PRT Simian immunodeficiency virus Deduced amino acid sequence of SIVrcm Nef protein 53 Met Gly Gly Lys Ser Ser Lys Asn Ser Ala Ala Gly Leu Leu Arg Trp 1 5 10 15 Arg Phe Lys Met Leu Thr Thr Pro Gly Glu Gly Tyr Val Arg Trp His 20 25 30 Glu Thr Leu Leu Asp Gly Gln Pro Trp Cys Ala Glu Gly Ser Gly Arg 35 40 45 Ala Ser Arg Asp Phe Val Ile Arg Gly Gly Ile Thr Ala Glu Thr Gln 50 55 60 Ala Ser Ile Asp Asp Ile Asp Trp Tyr Glu Asp Thr Asp Asp Thr Leu 65 70 75 80 Val Gly Phe Pro Val Lys Pro Gln Val Pro Leu Arg Pro Met Ser Tyr 85 90 95 Lys Leu Ala Ile Asp Met Ser His Phe Leu Lys Glu Lys Gly Gly Leu 100 105 110 Glu Gly Ile Tyr Trp Ser Ile Arg Arg Gln Arg Ile Leu Asp Met Tyr 115 120 125 Leu Glu Asn Glu His Gly Ile Ile Pro Asp Trp Gln Asn Tyr Thr Pro 130 135 140 Gly Pro Gly Ile Arg Tyr Pro Thr Leu Phe Gly Trp Leu Trp Gln Leu 145 150 155 160 Val Pro Val Asp Val Ser Asp Glu Ala Arg Glu Asp Glu Glu His Ser 165 170 175 Leu Leu His Pro Ala Glu Thr Ser Gly Met Glu Asp Pro Trp Gly Glu 180 185 190 Val Leu Ala Trp Lys Phe Asn Pro Met Leu Ala Val Asp Tyr Ile Gly 195 200 205 Tyr Arg Leu His Pro Glu Phe Phe Gly Glu Arg Lys Asn Lys Thr Gln 210 215 220 54 318 PRT Simian immunodeficiency virus Deduced amino acid sequence of SIVrcm gag gene 54 Lys Tyr Met Leu Lys His Leu Val Trp Ala Cys Lys Lys Leu Asn Lys 1 5 10 15 Phe Gly Leu Ser Asp His Leu Leu Glu Thr Ala Thr Gly Cys Glu Lys 20 25 30 Ile Leu Gly Val Leu Leu Pro Leu Val Pro Thr Gly Ser Glu Gly Leu 35 40 45 Lys Ser Leu Phe Asn Leu Cys Cys Val Leu Trp Cys Val His Lys Glu 50 55 60 Val Lys Val Lys Asp Thr Glu Glu Ala Val Ala Lys Val Lys Glu Cys 65 70 75 80 Cys His Leu Val Glu Lys Ala Glu Asn Thr Thr Glu Lys Glu Lys Gly 85 90 95 Ala Thr Ala Pro Pro Ser Gly Gln Arg Gly Asn Tyr Pro Ile Ile Thr 100 105 110 Ile Asn Gln Gln Pro Glu His Asn Pro Ile Ser Pro Arg Thr Leu Asn 115 120 125 Ala Trp Val Lys Val Val Glu Glu Lys Lys Phe Ser Ala Glu Val Ala 130 135 140 Pro Met Phe Ser Ala Leu Ser Glu Gly Cys Ile Pro Tyr Asp Ile Asn 145 150 155 160 Gln Met Leu Asn Ala Ile Gly Glu His Gln Gly Ala Leu Gln Ile Val 165 170 175 Lys Glu Val Ile Asn Glu Glu Ala Ala Asp Trp Asp Ala Arg His Pro 180 185 190 Val Pro Gly Pro Ile Pro Ala Gly Gln Leu Arg Glu Pro Thr Gly Ser 195 200 205 Asp Ile Ala Gly Thr Thr Ser Ser Ile Ala Glu Gln Ile Ala Trp Thr 210 215 220 Thr Arg Ala Asn Asn Pro Ile Asn Val Gly Asn Leu Tyr Arg Asn Trp 225 230 235 240 Ile Ile Val Gly Leu Gln Lys Trp Val Lys Met Tyr Asn Pro Val Asn 245 250 255 Ile Leu Asp Ile Lys Gln Gly Pro Lys Glu Ser Phe Lys Asp Tyr Val 260 265 270 Asp Arg Phe Tyr Lys Ala Leu Arg Ala Glu Gln Ala Asp Pro Ala Val 275 280 285 Lys Asn Trp Met Thr Gln Ser Leu Leu Ile Gln Asn Ala Asn Pro Asp 290 295 300 Cys Lys Met Val Leu Lys Gly Leu Gly Met Asn Pro Ser Leu 305 310 315 55 954 DNA Simian immunodeficiency virus Partial nucleotide sequence of SIVrcm gag gene; GenBank Accession No. AFn28608 55 aaatacatgc tgaagcattt ggtatgggca tgcaaaaaac taaataaatt tggcttgagt 60 gatcatttgt tagaaacagc aacaggatgt gaaaaaatat taggagtcct gctgcctcta 120 gttccgacag ggtcagaggg gctaaaaagc ctctttaatt tgtgctgcgt actctggtgc 180 gtacacaagg aagtgaaagt gaaagacaca gaggaagctg tagcaaaagt gaaagaatgc 240 tgccatctag tggaaaaagc agaaaataca acagaaaaag aaaagggagc aacagcgcca 300 cctagtggac aaagaggaaa ttatcctata attactataa atcagcagcc tgagcataat 360 cctatatcac caaggactct aaatgcctgg gtcaaggtgg tagaggagaa aaaattctca 420 gcagaagtag cgcccatgtt ctcggcacta tcagaaggct gcatacccta tgatataaat 480 caaatgctaa atgccatagg ggaacaccag ggtgcgctgc agatagtaaa ggaagtgatc 540 aatgaggaag cagcagactg ggatgctaga catccagtac caggcccgat accagcaggg 600 caacttagag aaccaacagg aagtgacata gcagggacaa ctagctcaat agcagaacag 660 atagcttgga ccaccagagc aaacaacccc attaatgtgg gcaatctgta cagaaattgg 720 ataatagtag ggttacaaaa atgggtaaaa atgtacaatc cagtgaacat cctagatata 780 aagcaaggac caaaagagtc attcaaggat tatgtggata gattttataa agccttgaga 840 gcagaacagg cagacccggc agtaaaaaat tggatgacac aatcactgct gatacaaaat 900 gctaacccag actgtaaaat ggtactcaag ggtctgggaa tgaacccttc ttta 954 56 158 PRT Simian immunodeficiency virus 148 Deduced amino acid sequence of SIVrcm pol gene; Xaa = unknown 56 Ile Pro Ala Glu Thr Gly Lys Glu Thr Ala Tyr Phe Leu Leu Lys Leu 1 5 10 15 Ala Ala Arg Trp Pro Val Arg Lys Leu His Thr Asp Asn Gly Ala Asn 20 25 30 Phe Thr Ser Ala Ala Val Gln Ala Val Cys Trp Trp Ala Gln Ile Glu 35 40 45 His Thr Phe Gly Val Pro Tyr Asn Pro Gln Ser Gln Gly Val Val Glu 50 55 60 Ser Met Asn Lys Gln Leu Lys Ile Ile Ile Glu Gln Val Arg Glu Gln 65 70 75 80 Ala Glu Lys Leu Glu Thr Ala Val Gln Met Ala Val Leu Val His Asn 85 90 95 Phe Lys Arg Lys Gly Gly Ile Gly Gly Tyr Ser Ala Gly Glu Arg Ile 100 105 110 Ile Asp Ile Ile Ala Thr Asp Leu Ala Thr Asn Lys Leu Gln Asn Gln 115 120 125 Ile Ser Lys Ile Gln Asn Phe Arg Val Tyr Tyr Arg Glu Gly Arg Asp 130 135 140 Gln Leu Trp Xaa Gly Pro Ala Lys Leu Ile Trp Lys Gly Glu 145 150 155 57 475 DNA Simian immunodeficiency virus 444 Partial nucleotide sequence of SIVrcm pol gene; n = unknown; GenBank Accession No. AFn28607 57 aataccagca gaaacaggaa aagagacagc atatttcctg ttgaaactag cagcaagatg 60 gccagtaagg aagctacaca cagataatgg agcaaatttc acaagtgcag cagtacaggc 120 ggtctgctgg tgggctcaga tagagcacac ctttggagta ccttacaatc ctcaaagtca 180 aggagtagtg gaaagcatga ataaacaatt aaaaataatc atagaacaag taagagaaca 240 agcagaaaaa ttagaaacag cagtccaaat ggcagttttg gttcacaatt ttaaaagaaa 300 aggggggatt ggggggtaca gtgcaggaga aagaataata gatataatag caacagactt 360 agcaaccaat aaattacaaa atcaaatttc aaaaattcaa aattttcggg tttattacag 420 agaaggaagg gatcaactgt gganaggtcc agctaagctg atctggaaag gtgaa 475 58 52 RNA Simian immunodeficiency virus stem_loop Nucleotide sequence of SIVrcm LTR sequence having a duplicated TAR stemloop structure 58 ccggauugag ccuggguguu cucuggccag cuugagccug gguguucgcu gg 52 

What is claimed is:
 1. A nucleic acid comprising the nucleotide sequence of the genome of the simian immunodeficiency virus isolate SIVrcm shown in SEQ ID NO:1 or a complementary sequence thereof.
 2. The nucleic acid of claim 1, wherein said nucleic acid comprises a nucleotide sequence of at least 12 contiguous bases of said nucleic acid or a complementary sequence thereof.
 3. The nucleic acid of claim 1, wherein said nucleic acid comprises a nucleotide sequence of a LTR of said nucleic acid or a complementary sequence thereof.
 4. The nucleic acid of claim 1, wherein said nucleic acid encodes a polypeptide selected from the group consisting of Gag, Pol, Vif, Vpr, Env, Tat, Rev, Nef and Vpx of SIVrcm.
 5. The nucleic acid of claim 1, wherein said nucleic acid has a nucleotide sequence which is derived from SEQ ID NO:1.
 6. A vector comprising the nucleic acid of claim
 1. 7. A cell comprising the nucleic acid of claim
 1. 8. A cell comprising the vector of claim
 6. 9. A composition comprising the nucleic acid of claim 1 and a physiologically acceptable carrier.
 10. A method for producing a polypeptide encoded by the nucleic acid of claim 1, comprising the step of growing a cell comprising the nucleic acid of claim 1 under conditions such that the encoded polypeptide is produced.
 11. The method of claim 10, wherein said polypeptide comprises a contiguous sequence of at least 13 amino acids.
 12. A composition comprising the polypeptide produced by the method of claim 10 and a physiologically acceptable carrier.
 13. A method for producing a polypeptide encoded by the nucleic acid of claim 1, comprising the step of growing a cell comprising a vector, said vector comprising the nucleic acid of claim 1, under conditions such that the encoded polypeptide is produced.
 14. The method of claim 13, wherein said polypeptide comprises a contiguous sequence of at least 13 amino acids.
 15. A composition comprising the polypeptide produced by the method of claim 13 and a physiologically acceptable carrier.
 16. A method of inducing serum antibodies that bind at least one polypeptide encoded by the nucleic acid of claim 1, said method comprising: administering to a mammal, in a physiologically acceptable carrier, an amount of said encoded polypeptide sufficient to elicit production of said antibodies.
 17. An anti-SIVrcm antibody made by the method of claim
 16. 18. A composition comprising an antibody according to claim 17 and a physiologically acceptable carrier.
 19. A method for detecting the presence of SIVrcm in a sample comprising contacting said sample with the antibody of claim 17 under conditions that allow the formation of an antibody-antigen complex and detecting said complex.
 20. A kit for detecting the presence of SIVrcm in a sample comprising an antibody of claim
 17. 21. A method of inducing serum antibodies that bind at least one polypeptide encoded by the nucleic acid of claim 1, said method comprising: administering to a mammal, in a physiologically acceptable carrier, the nucleic acid of claim 1 encoding said polypeptide and which produces an immunologically sufficient amount of the encoded polypeptide to elicit said antibodies.
 22. An antibody to SIVrcm made by the method of claim
 21. 23. A composition comprising an antibody according to claim 22, and a physiologically acceptable carrier.
 24. A method for detecting the presence of SIVrcm in a sample comprising contacting said sample with the antibody of claim 22 under conditions that allow the formation of an antibody-antigen complex and detecting said complex.
 25. A kit for detecting the presence of SIVrcm in a sample comprising an antibody of claim
 22. 26. A method for detecting the presence of antibodies to SIVrcm in a sample comprising contacting said sample with a polypeptide encoded by the nucleic acid of claim 1 under conditions that allow the formation of an antibody-antigen complex and detecting the complex.
 27. A method for detecting the presence of SIVrcm in a sample comprising contacting said sample with the nucleic acid of claim 1 and detecting said nucleic acid bound to the genomic DNA, mRNA or cDNA of the SIVrcm virus.
 28. A kit for detecting the presence of SIVrcm in a sample comprising the nucleic acid of claim
 1. 29. A nucleic acid probe comprising a sequence of at least 19 contiguous nucleotides derived from the nucleic acid of claim 1, or the complementary sequence thereof.
 30. A composition comprising a nucleic acid according to claim
 29. 31. A method of detecting the presence of SIVrcm in a biological sample comprising: a.) contacting the nucleic acid of the biological sample with the nucleic acid probe of claim 29; and b.) detecting the presence or absence of complexes formed between said nucleic acid of the biological sample and said nucleic acid probe.
 32. A method of detecting the presence of SIVrcm in a biological sample comprising: a). contacting said biological sample with at least two nucleic acid probes of claim 29; b). amplifying the RNA of the biological sample via reverse transcription-polymerase chain reaction to produce amplification products; and c.) detecting the presence or absence of amplification products.
 33. A method for analyzing a first nucleotide sequence comprising comparing the nucleotide sequence of claim 1 with said first sequence. 